match no. | target id | target length | alignment length | probability | E-value | coverage | match description |
1 | COG0675 | 364 | 240 | 99.9 | 4.6E-22 | [ ------------------------------------------] | InsQ | Transposase |
2 | pfam07282 | 69 | 61 | 99.8 | 7.3E-20 | [ ---------] | OrfB_Zn_ribbon | Putative transposase DNA-binding domain. This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesise this domain is DNA-binding. |
3 | pfam01385 | 226 | 161 | 99.3 | 4.3E-11 | [ --------------------------- ] | OrfB_IS605 | Probable transposase. This family includes IS891, IS1136 and IS1341. DUF1225, pfam06774, has now been merged into this family. |
4 | TIGR01766 | 82 | 57 | 99.1 | 3.7E-10 | [ --------- ] | tspaseT_teng_C | transposase, IS605 OrfB family, central region. This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam01385, and other proteins. |
5 | COG2888 | 61 | 41 | 94.2 | 0.018 | [ ------ ] | COG2888 | Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 family |
6 | PRK12286 | 57 | 32 | 93.6 | 0.035 | [ -----] | rpmF | 50S ribosomal protein L32; Reviewed |
7 | pfam09538 | 104 | 37 | 92.6 | 0.055 | [ ------] | FYDLN_acid | Protein of unknown function (FYDLN_acid). Members of this family are bacterial proteins with a conserved motif |
8 | pfam10571 | 26 | 24 | 91.9 | 0.05 | [ ---- ] | UPF0547 | Uncharacterized protein family UPF0547. This domain contains a zinc-ribbon motif. |
9 | PRK00432 | 50 | 27 | 91.3 | 0.072 | [ ---- ] | PRK00432 | 30S ribosomal protein S27ae; Validated |
10 | TIGR04165 | 50 | 30 | 90.7 | 0.12 | [ ---- ] | methano_modCys | Cys-rich peptide, TIGR04165 family. Members of this small peptide family occur strictly in a subset of archaeal methanogens. Members have four invariant Cys residues in two Cys-Xaa-Xaa-Cys-Gly motifs and may have other Cys residues as well. At least two members occur next to family TIGR04083 radical SAM enzymes predicted to act in peptide or protein modification. |
11 | COG1645 | 131 | 35 | 90.4 | 0.14 | [ ------- ] | COG1645 | Uncharacterized Zn-finger containing protein, UPF0148 family |
12 | cd00656 | 45 | 31 | 90.3 | 0.14 | [ ---- ] | Zn-ribbon | C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit. The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II. |
13 | COG1998 | 51 | 28 | 90.3 | 0.11 | [ ---- ] | RPS27AE | Ribosomal protein S27AE |
14 | cd10511 | 47 | 31 | 89.5 | 0.15 | [ ---- ] | Zn-ribbon_TFS | C-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS). TFS is an archaeal protein that stimulates the intrinsic cleavage activity of archaeal RNA polymerase. TFS C-terminal domain shows sequence similarity to the homologous C-terminal zinc ribbon domain of subunits A12.2, Rpb9, and C11 in eukaryotic RNA Polymerases (Pol) I, II, and III, respectively and domain III of TFIIS. TFS is not a subunit of archaeal RNA polymerase even though its domains arrangement is similar to A12.2, Rpb9, and C1. TFS is a transcription factor with a similar function to eukaryotic TFIIS. TFS has external cleavage induction activity and improves the fidelity of transcription. TFS has two zinc-binding domains. |
15 | PRK14890 | 59 | 26 | 88.4 | 0.2 | [ ---- ] | PRK14890 | putative Zn-ribbon RNA-binding protein; Provisional |
16 | pfam07754 | 18 | 11 | 87.6 | 0.22 | [ - ] | DUF1610 | Domain of unknown function (DUF1610). This zinc ribbon domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues. |
17 | PRK14890 | 59 | 41 | 86.1 | 0.46 | [ ------ ] | PRK14890 | putative Zn-ribbon RNA-binding protein; Provisional |
18 | pfam13240 | 23 | 21 | 86.0 | 0.28 | [ ---- ] | zinc_ribbon_2 | zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. pfam12773. |
19 | TIGR04330 | 1286 | 124 | 85.7 | 2.4 | [ -------------------- ] | cas_Cpf1 | CRISPR-associated protein Cpf1, subtype PREFRAN. This family is the long protein of a novel CRISPR subtype, PREFRAN, which is most common in Prevotella and Francisella, although widely distributed. The PREFRAN type has Cas1, Cas2, and Cas4, but lacks the helicase Cas3 and endonuclease Cas3-HD. |
20 | pfam09297 | 32 | 29 | 85.1 | 0.55 | [ ---- ] | zf-NADH-PPase | NADH pyrophosphatase zinc ribbon domain. This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure. |
21 | COG2888 | 61 | 26 | 84.8 | 0.49 | [ ---- ] | COG2888 | Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 family |
22 | PRK08173 | 862 | 80 | 84.8 | 0.86 | [ ------------- ] | PRK08173 | DNA topoisomerase III; Validated |
23 | COG1996 | 49 | 30 | 84.3 | 0.54 | [ ---- ] | RPC10 | DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger |
24 | COG3357 | 97 | 44 | 83.9 | 0.72 | [ --------] | COG3357 | Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon |
25 | pfam08274 | 30 | 27 | 83.5 | 0.67 | [ -----] | PhnA_Zn_Ribbon | PhnA Zinc-Ribbon. |
26 | COG1096 | 188 | 29 | 83.4 | 0.52 | [ -----] | Csl4 | Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains |
27 | PRK00420 | 112 | 38 | 82.6 | 0.76 | [ ------- ] | PRK00420 | hypothetical protein; Validated |
28 | TIGR01031 | 55 | 30 | 82.0 | 0.75 | [ -----] | rpmF_bact | ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus. |
29 | PRK04179 | 62 | 33 | 80.6 | 0.63 | [ -----] | rpl37e | 50S ribosomal protein L37e; Reviewed |
30 | pfam13248 | 26 | 24 | 79.5 | 0.77 | [ ---- ] | zf-ribbon_3 | zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. pfam12773. |
31 | pfam09151 | 36 | 27 | 78.9 | 1.1 | [ ---- ] | DUF1936 | Domain of unknown function (DUF1936). This domain is found in a set of hypothetical Archaeal proteins. Its exact function has not, as yet, been defined. It possesses a zinc ribbon fold. |
32 | COG2126 | 61 | 35 | 78.5 | 0.91 | [ -----] | RPL37A | Ribosomal protein L37E |
33 | PRK14892 | 99 | 13 | 78.0 | 1.2 | [ -- ] | PRK14892 | putative transcription elongation factor Elf1; Provisional |
34 | COG2816 | 279 | 34 | 77.6 | 1 | [ ----- ] | NPY1 | NADH pyrophosphatase NudC, Nudix superfamily |
35 | pfam13453 | 41 | 25 | 76.9 | 1.2 | [ ---- ] | zf-TFIIB | Transcription factor zinc-finger. |
36 | pfam01783 | 56 | 30 | 76.7 | 1.2 | [ -----] | Ribosomal_L32p | Ribosomal L32p protein family. |
37 | COG0333 | 57 | 31 | 76.3 | 1.5 | [ -----] | RpmF | Ribosomal protein L32 |
38 | PRK09521 | 189 | 30 | 76.1 | 1.4 | [ -----] | PRK09521 | exosome complex RNA-binding protein Csl4; Provisional |
39 | COG1579 | 239 | 30 | 75.3 | 14 | [ -----] | COG1579 | Predicted nucleic acid-binding protein, contains Zn-ribbon domain |
40 | PRK09401 | 1176 | 41 | 75.1 | 1.1 | [ -------] | PRK09401 | reverse gyrase; Reviewed |
41 | cd13946 | 54 | 27 | 75.0 | 1.7 | [ ---- ] | LysW | Lysine biosynthesis protein LysW. LysW functions as a carrier protein in the biosynthesis pathway of lysine. The C-terminal glutamate sidechain of LysW attaches to the amino group of alpha-aminoadipate (AAA); this peptide bond formation is catalyzed by the ligase LysX. AAA remains associated with LysW throughout its biosynthetic conversion to lysine. LysW also acts to protect the amino group of glutamate in arginine biosynthesis. |
42 | PRK14892 | 99 | 38 | 74.8 | 1.2 | [ ------] | PRK14892 | putative transcription elongation factor Elf1; Provisional |
43 | pfam12760 | 46 | 32 | 74.8 | 1.8 | [ ----- ] | Zn_Tnp_IS1595 | Transposase zinc-ribbon domain. This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It is likely a zinc-binding beta ribbon domain that could bind the DNA. |
44 | cd00729 | 34 | 26 | 74.6 | 1.1 | [ -----] | rubredoxin_SM | Rubredoxin, Small Modular nonheme iron binding domain containing a |
45 | COG4888 | 104 | 42 | 74.3 | 1.6 | [ ------] | Elf1 | Transcription elongation factor Elf1, contains Zn-ribbon domain |
46 | pfam02150 | 35 | 29 | 74.3 | 1.8 | [ -----] | RNA_POL_M_15KD | RNA polymerases M/15 Kd subunit. |
47 | pfam08271 | 41 | 29 | 73.7 | 1.8 | [ -----] | TF_Zn_Ribbon | TFIIB zinc-binding. The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure. |
48 | COG1592 | 166 | 22 | 73.5 | 2.3 | [ ---- ] | YotD | Rubrerythrin |
49 | pfam03604 | 32 | 25 | 73.3 | 1.9 | [ ---- ] | DNA_RNApol_7kD | DNA directed RNA polymerase, 7 kDa subunit. |
50 | pfam14803 | 34 | 26 | 72.7 | 1.6 | [ ---- ] | Nudix_N_2 | Nudix N-terminal. Ths domain occurs at the N-terminus of several Nudix (Nucleoside Diphosphate linked to X) hydrolases. |
51 | pfam03833 | 852 | 55 | 72.4 | 1.4 | [ --------- ] | PolC_DP2 | DNA polymerase II large subunit DP2. |
52 | COG4530 | 129 | 34 | 72.4 | 1.5 | [ -----] | COG4530 | Uncharacterized protein |
53 | PRK03976 | 90 | 27 | 71.8 | 1.7 | [ ---- ] | rpl37ae | 50S ribosomal protein L37Ae; Reviewed |
54 | TIGR00467 | 515 | 46 | 71.7 | 4.4 | [ -------] | lysS_arch | lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set. |
55 | COG1571 | 421 | 35 | 71.1 | 1.6 | [ ------] | TiaS | tRNA(Ile2) C34 agmatinyltransferase TiaS |
56 | COG1997 | 89 | 26 | 69.9 | 2.2 | [ ---- ] | RPL43A | Ribosomal protein L37AE/L43A |
57 | TIGR04104 | 94 | 29 | 69.9 | 1.4 | [ -----] | cxxc_20_cxxc | cxxc_20_cxxc protein. This small, uncommon, poorly conserved protein is found primarily in the Firmicutes. It features are pair of CxxC motifs separated by about 20 amino acids, followed by a highly hydrophobic region of about 45 amino acids. It has no conserved gene neighborhood, and its function is unknown. |
58 | pfam13597 | 543 | 38 | 69.7 | 3.1 | [ ------- ] | NRDD | Anaerobic ribonucleoside-triphosphate reductase. |
59 | pfam13719 | 37 | 29 | 69.2 | 2.4 | [ ---- ] | zinc_ribbon_5 | zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR, pfam12773. |
60 | cd03361 | 170 | 30 | 68.3 | 2.1 | [ ----- ] | TOPRIM_TopoIA_RevGyr | TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. |
61 | pfam06677 | 41 | 32 | 67.9 | 2.3 | [ ------ ] | Auto_anti-p27 | Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis. |
62 | PRK00398 | 46 | 27 | 67.5 | 2 | [ ---- ] | rpoP | DNA-directed RNA polymerase subunit P; Provisional |
63 | pfam10058 | 51 | 36 | 66.7 | 4.3 | [ ----- ] | DUF2296 | Predicted integral membrane metal-binding protein (DUF2296). This domain, found in various hypothetical bacterial and eukaryotic metal-binding proteins, has no known function. |
64 | cd00350 | 33 | 24 | 64.9 | 2.6 | [ ---- ] | rubredoxin_like | Rubredoxin_like; nonheme iron binding domain containing a |
65 | TIGR00515 | 285 | 27 | 62.2 | 2.7 | [ ---- ] | accD | acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta. |
66 | TIGR00280 | 92 | 25 | 62.2 | 4.1 | [ ---- ] | eL43_euk_arch | ribosomal protein eL43. This model finds eukaryotic ribosomal protein eL43 (previously L37a) and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a. |
67 | PRK00241 | 256 | 35 | 62.2 | 3.7 | [ ----- ] | nudC | NADH pyrophosphatase; Reviewed |
68 | PRK05654 | 292 | 28 | 61.9 | 2.2 | [ ---- ] | PRK05654 | acetyl-CoA carboxylase subunit beta; Validated |
69 | TIGR01206 | 54 | 29 | 61.8 | 4.1 | [ ---- ] | lysW | lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway. |
70 | TIGR02098 | 38 | 29 | 61.1 | 4.4 | [ ---- ] | MJ0042_CXXC | MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility. |
71 | pfam13717 | 36 | 29 | 60.4 | 4.5 | [ ---- ] | zinc_ribbon_4 | zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR, pfam12773. |
72 | pfam07295 | 148 | 43 | 60.3 | 3.3 | [ ------- ] | DUF1451 | Protein of unknown function (DUF1451). This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown. |
73 | cd09680 | 650 | 27 | 58.6 | 49 | [ ---- ] | Cas10_III | CRISPR/Cas system-associated protein Cas10. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Multidomain protein with permuted HD nuclease domain, palm domain and Zn-ribbon; signature gene for type III; also known as Csm1 family |
74 | COG1594 | 113 | 32 | 57.8 | 5.1 | [ -----] | RPB9 | DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS |
75 | pfam12773 | 45 | 27 | 57.8 | 6.6 | [ -----] | DZR | Double zinc ribbon. This family consists of a pair of zinc ribbon domains. |
76 | cd10509 | 46 | 31 | 57.2 | 5.3 | [ ---- ] | Zn-ribbon_RPC11 | C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III. The C-terminal zinc ribbon domain (C_ribbon) of subunit C11 (C-ribbon_RPC11) in RNA polymerase (Pol) III is required for intrinsic transcript cleavage. RPC11 is also involved in Pol III termination. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPC11 have strong homology to RPB9 of Pol II and RPA12 of Pol I. C-ribbon_RPC11 is homologous to Pol II elongation factor TFIIS domain III. C11 has two zinc-binding domains separated by a flexible linker. |
77 | COG1110 | 1187 | 32 | 57.2 | 4.1 | [ ------] | TopG2 | Reverse gyrase |
78 | PRK08270 | 656 | 41 | 56.4 | 4.6 | [ --------] | PRK08270 | anaerobic ribonucleoside triphosphate reductase; Provisional |
79 | TIGR01384 | 104 | 35 | 56.3 | 5.6 | [ ----- ] | TFS_arch | transcription factor S, archaeal. This model describes archaeal transcription factor S, a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae. |
80 | pfam13824 | 54 | 23 | 55.6 | 5.1 | [ ---- ] | zf-Mss51 | Zinc-finger of mitochondrial splicing suppressor 51. Mss51 regulates the expression of cytochrome oxidase, so this domain is probably DNA-binding. |
81 | TIGR02300 | 129 | 31 | 54.7 | 5.4 | [ ----- ] | FYDLN_acid | TIGR02300 family protein. Members of this family are bacterial proteins with a conserved motif |
82 | COG2956 | 389 | 66 | 54.4 | 6.3 | [ ------------ ] | YciM | Lipopolysaccharide biosynthesis regulator YciM, contains six TPR domains and a predicted metal-binding C-terminal domain |
83 | pfam09723 | 43 | 30 | 53.5 | 4.8 | [ -----] | Zn-ribbon_8 | Zinc ribbon domain. This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence. |
84 | PRK01103 | 274 | 101 | 53.3 | 5.2 | [ ---------------- ] | PRK01103 | formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated |
85 | pfam14446 | 55 | 34 | 51.7 | 10 | [ ------] | Prok-RING_1 | Prokaryotic RING finger family 1. RING finger family found sporadically in bacteria and archaea, and associated in gene neighborhoods with other components of the ubiquitin-based signaling and degradation system, including ubiquitin, the E1 and E2 proteins and the JAB-like metallopeptidase. The bacterial versions contain transmembrane helices. |
86 | COG1379 | 403 | 34 | 50.7 | 5.4 | [ ------] | YqxK | PHP family phosphoesterase with a Zn ribbon |
87 | PRK12336 | 201 | 30 | 49.8 | 6.4 | [ ---- ] | PRK12336 | translation initiation factor IF-2 subunit beta; Provisional |
88 | pfam02591 | 56 | 28 | 49.4 | 6.2 | [ ---- ] | DUF164 | Putative zinc ribbon domain. Structural modelling suggests this domain may bind nucleic acids. |
89 | PRK14714 | 1337 | 89 | 48.7 | 8.1 | [ --------------- ] | PRK14714 | DNA polymerase II large subunit; Provisional |
90 | cd04476 | 166 | 29 | 48.3 | 9.5 | [ ---- ] | RPA1_DBD_C | RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding function of this domain. It appears that zinc itself may not be required for ssDNA binding. |
91 | cd10507 | 47 | 31 | 47.7 | 9.9 | [ ---- ] | Zn-ribbon_RPA12 | C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I. The C-terminal zinc ribbon domain (C_ribbon) of subunit A12 (C-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker. |
92 | PRK03988 | 138 | 32 | 47.5 | 7 | [ -----] | PRK03988 | translation initiation factor IF-2 subunit beta; Validated |
93 | PRK14715 | 1627 | 21 | 47.3 | 9.6 | [ ---- ] | PRK14715 | DNA polymerase II large subunit; Provisional |
94 | COG0266 | 273 | 28 | 47.1 | 7.3 | [ ---- ] | Nei | Formamidopyrimidine-DNA glycosylase |
95 | COG1545 | 140 | 26 | 47.1 | 8.1 | [ ---- ] | COG1545 | Uncharacterized OB-fold protein, contains Zn-ribbon domain |
96 | PRK07225 | 605 | 31 | 47.1 | 8.2 | [ -----] | PRK07225 | DNA-directed RNA polymerase subunit B'; Validated |
97 | COG0777 | 294 | 27 | 46.7 | 5.1 | [ ---- ] | AccD | Acetyl-CoA carboxylase beta subunit |
98 | pfam06827 | 30 | 26 | 46.1 | 8.3 | [ ---- ] | zf-FPG_IleRS | Zinc finger found in FPG and IleRS. This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23. |
99 | PRK03954 | 121 | 16 | 45.8 | 5.8 | [ -- ] | PRK03954 | ribonuclease P protein component 4; Validated |
100 | PRK09263 | 711 | 29 | 45.7 | 8.3 | [ ---- ] | PRK09263 | anaerobic ribonucleoside triphosphate reductase; Provisional |
101 | COG2093 | 64 | 25 | 45.6 | 10 | [ ---- ] | Spt4 | RNA polymerase subunit RPABC4/transcription elongation factor Spt4 |
102 | TIGR02487 | 579 | 44 | 45.4 | 16 | [ -------- ] | NrdD | anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer. |
103 | TIGR00354 | 1095 | 26 | 45.1 | 9.4 | [ -----] | polC | DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. |
104 | PRK12495 | 226 | 63 | 45.1 | 30 | [ -------------] | PRK12495 | hypothetical protein; Provisional |
105 | COG1328 | 700 | 40 | 44.8 | 18 | [ ------- ] | NrdD | Anaerobic ribonucleoside-triphosphate reductase |
106 | TIGR02605 | 52 | 31 | 44.7 | 9 | [ -----] | CxxC_CxxC_SSSS | putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (SP:Q50229, ). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors. |
107 | PRK04011 | 411 | 32 | 44.1 | 8.5 | [ -----] | PRK04011 | peptide chain release factor 1; Provisional |
108 | PRK08579 | 625 | 26 | 43.9 | 9.5 | [ ---- ] | PRK08579 | anaerobic ribonucleoside triphosphate reductase; Provisional |
109 | PRK07418 | 616 | 25 | 43.6 | 9.4 | [ ---- ] | PRK07418 | acetolactate synthase 3 catalytic subunit; Reviewed |
110 | pfam14354 | 56 | 31 | 43.5 | 11 | [ ---- ] | Lar_restr_allev | Restriction alleviation protein Lar. This family includes the restriction alleviation protein Lar encoded by the Rac prophage of Escherichia coli. This protein modulates the activity of the Escherichia coli restriction and modification system. |
111 | PRK14282 | 369 | 30 | 42.9 | 12 | [ ----- ] | PRK14282 | chaperone protein DnaJ; Provisional |
112 | PRK14714 | 1337 | 43 | 42.5 | 10 | [ -------] | PRK14714 | DNA polymerase II large subunit; Provisional |
113 | COG0375 | 115 | 27 | 42.4 | 10 | [ -----] | HybF | Hydrogenase maturation metallochaperone HypA/HybF, involved in Ni insertion |
114 | PRK13208 | 800 | 37 | 42.1 | 11 | [ ------] | valS | valyl-tRNA synthetase; Reviewed |
115 | PRK12366 | 637 | 32 | 41.9 | 11 | [ -----] | PRK12366 | replication factor A; Reviewed |
116 | cd02582 | 861 | 15 | 41.9 | 8.3 | [ ---] | RNAP_archeal_A' | A' subunit of archaeal RNA polymerase (RNAP). A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins. |
117 | pfam01907 | 54 | 34 | 41.7 | 11 | [ -----] | Ribosomal_L37e | Ribosomal protein L37e. This family includes ribosomal protein L37 from eukaryotes and archaebacteria. The family contains many conserved cysteines and histidines suggesting that this protein may bind to zinc. |
118 | COG1656 | 165 | 30 | 41.1 | 12 | [ ---- ] | COG1656 | Uncharacterized conserved protein, contains PIN domain |
119 | TIGR03670 | 599 | 30 | 40.9 | 12 | [ -----] | rpoB_arch | DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes. |
120 | cd01675 | 555 | 45 | 40.3 | 11 | [ -------- ] | RNR_III | Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit which contains the active and allosteric sites. |
121 | PRK12268 | 556 | 13 | 39.8 | 21 | [ - ] | PRK12268 | methionyl-tRNA synthetase; Reviewed |
122 | PRK06556 | 953 | 24 | 39.8 | 13 | [ ---- ] | PRK06556 | vitamin B12-dependent ribonucleotide reductase; Validated |
123 | pfam01096 | 39 | 28 | 39.4 | 15 | [ ---- ] | TFIIS_C | Transcription factor S-II (TFIIS). |
124 | TIGR03676 | 403 | 31 | 39.1 | 12 | [ ---- ] | aRF1/eRF1 | peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1. |
125 | pfam14577 | 235 | 64 | 38.8 | 18 | [ ---------- ] | SEO_C | Sieve element occlusion C-terminus. Sieve element occlusion (SEO) proteins, or forisomes, are phloem proteins which accumulate during sieve element differentiation. This domain represents the C-terminus of SEO proteins. |
126 | pfam01780 | 90 | 27 | 37.7 | 15 | [ ---- ] | Ribosomal_L37ae | Ribosomal L37ae protein family. This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc. |
127 | COG1198 | 730 | 28 | 37.4 | 14 | [ ----- ] | PriA | Primosomal protein N' (replication factor Y) - superfamily II helicase |
128 | COG1384 | 521 | 42 | 37.4 | 15 | [ -------] | LysS | Lysyl-tRNA synthetase, class I |
129 | PRK14278 | 378 | 20 | 37.3 | 12 | [ ---- ] | PRK14278 | chaperone protein DnaJ; Provisional |
130 | PRK04136 | 48 | 28 | 37.1 | 18 | [ -----] | rpl40e | 50S ribosomal protein L40e; Provisional |
131 | pfam05876 | 557 | 32 | 37.0 | 18 | [ -----] | Terminase_GpA | Phage terminase large subunit (GpA). This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities. |
132 | COG2870 | 467 | 58 | 36.8 | 12 | [ ------------ ] | RfaE | ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase |
133 | COG5204 | 112 | 29 | 36.5 | 13 | [ ---- ] | SPT4 | Transcription elongation factor SPT4 |
134 | COG5179 | 968 | 42 | 36.4 | 55 | [ ------- ] | TAF1 | Transcription initiation factor TFIID, subunit TAF1 |
135 | pfam09855 | 64 | 13 | 36.0 | 17 | [ -- ] | DUF2082 | Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082). This domain, found in various hypothetical prokaryotic proteins, as well as some Zn-ribbon nucleic-acid-binding proteins has no known function. |
136 | TIGR00577 | 272 | 105 | 35.9 | 13 | [ ----------------- ] | fpg | DNA-formamidopyrimidine glycosylase. All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). |
137 | cd07157 | 86 | 29 | 35.7 | 8.8 | [ -----] | 2DBD_NR_DBD1 | The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown. |
138 | PRK04023 | 1121 | 103 | 35.5 | 17 | [ ------------------ ] | PRK04023 | DNA polymerase II large subunit; Validated |
139 | pfam05129 | 74 | 35 | 35.3 | 25 | [ -----] | Elf1 | Transcription elongation factor Elf1 like. This family of short proteins contains a putative zinc binding domain with four conserved cysteines. ELF1 has been identified as a transcription elongation factor in Saccharomyces cerevisiae. |
140 | PRK08566 | 882 | 15 | 34.8 | 13 | [ ---] | PRK08566 | DNA-directed RNA polymerase subunit A'; Validated |
141 | PRK11032 | 160 | 33 | 34.7 | 18 | [ ----- ] | PRK11032 | hypothetical protein; Provisional |
142 | PRK05580 | 679 | 48 | 34.7 | 16 | [ ------- ] | PRK05580 | primosome assembly protein PriA; Validated |
143 | PRK00390 | 805 | 17 | 34.6 | 14 | [ --] | leuS | leucyl-tRNA synthetase; Validated |
144 | pfam08209 | 33 | 11 | 34.3 | 23 | [ - ] | Sgf11 | Sgf11 (transcriptional regulation protein). The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae. The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation. |
145 | pfam05810 | 58 | 28 | 34.3 | 6.1 | [ -----] | NinF | NinF protein. This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli. |
146 | PRK05582 | 650 | 42 | 34.0 | 46 | [ ------- ] | PRK05582 | DNA topoisomerase I; Validated |
147 | TIGR03655 | 53 | 30 | 33.7 | 27 | [ -----] | anti_R_Lar | restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes. |
148 | pfam08273 | 39 | 31 | 33.1 | 27 | [ -----] | Prim_Zn_Ribbon | Zinc-binding domain of primase-helicase. |
149 | pfam05265 | 60 | 34 | 32.6 | 13 | [ ----- ] | DUF723 | Protein of unknown function (DUF723). This family contains several uncharacterized proteins from Neisseria meningitidis. These proteins may have a role in DNA-binding. |
150 | TIGR00373 | 158 | 27 | 32.2 | 9.5 | [ ---- ] | TIGR00373 | transcription factor E. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. |
151 | COG3677 | 129 | 50 | 32.1 | 34 | [ ---------] | InsA | Transposase |
152 | pfam01921 | 355 | 38 | 31.6 | 18 | [ ------] | tRNA-synt_1f | tRNA synthetases class I (K). This family includes only lysyl tRNA synthetases from prokaryotes. |
153 | pfam13465 | 26 | 13 | 31.6 | 23 | [ -- ] | zf-H2C2_2 | Zinc-finger double domain. |
154 | PRK08271 | 623 | 50 | 31.2 | 31 | [ --------- ] | PRK08271 | anaerobic ribonucleoside triphosphate reductase; Provisional |
155 | TIGR01054 | 1171 | 33 | 30.8 | 18 | [ ------] | rgy | reverse gyrase. This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA. |
156 | TIGR02390 | 868 | 15 | 30.7 | 14 | [ ---] | RNA_pol_rpoA1 | DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. |
157 | pfam01155 | 113 | 32 | 30.4 | 21 | [ ------] | HypA | Hydrogenase expression/synthesis hypA family. Four conserved cysteines lie either side of the least conserved region. |
158 | COG3809 | 88 | 26 | 30.2 | 23 | [ ---- ] | COG3809 | Predicted nucleic acid-binding protein, contains Zn-finger domain |
159 | cd07167 | 93 | 22 | 29.9 | 16 | [ ---- ] | NR_DBD_Lrh-1_like | The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not yet been identified. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 and SF-1 bind to DNA as monomers. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, receptors in this family have a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). |
160 | pfam04606 | 47 | 26 | 29.7 | 24 | [ ---- ] | Ogr_Delta | Ogr/Delta-like zinc finger. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F. This family also includes zinc fingers in recombinase proteins. |
161 | pfam14620 | 360 | 59 | 29.4 | 16 | [ --------- ] | YPEB | YpeB sporulation. YPEB is a protein that is necessary for the functioning of SleB during spore-cortex hydrolysis. |
162 | pfam13005 | 46 | 15 | 29.3 | 29 | [ -- ] | zf-IS66 | zinc-finger binding domain of transposase IS66. This is a zinc-finger region of the N-terminus of the insertion element IS66 transposase. |
163 | cd15728 | 63 | 30 | 29.2 | 22 | [ ----- ] | FYVE_ANFY1 | FYVE domain found in ankyrin repeat and FYVE domain-containing protein 1 (ANFY1) and similar proteins. ANFY1, also termed ankyrin repeats hooked to a zinc finger motif (Ankhzn), is a novel cytoplasmic protein that belongs to a new group of double zinc finger proteins involved in vesicle or protein transport. It is ubiquitously expressed in a spatiotemporal-specific manner and is located on endosomes. ANFY1 contains an N-terminal coiled-coil region and a BTB/POZ domain, ankyrin repeats in the middle, and a C-terminal FYVE domain. |
164 | COG1601 | 151 | 31 | 29.2 | 10 | [ ---- ] | GCD7 | Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain |
165 | PRK08665 | 752 | 27 | 28.4 | 28 | [ ---- ] | PRK08665 | ribonucleotide-diphosphate reductase subunit alpha; Validated |
166 | COG5349 | 126 | 28 | 28.3 | 16 | [ ---- ] | COG5349 | Uncharacterized conserved protein, DUF983 family |
167 | PRK14724 | 987 | 51 | 27.9 | 62 | [ -------- ] | PRK14724 | DNA topoisomerase III; Provisional |
168 | PRK14283 | 378 | 30 | 27.5 | 27 | [ ---- ] | PRK14283 | chaperone protein DnaJ; Provisional |
169 | cd00674 | 353 | 39 | 27.4 | 31 | [ ------] | LysRS_core_class_I | catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity. |
170 | PRK13945 | 282 | 34 | 27.3 | 24 | [ ----- ] | PRK13945 | formamidopyrimidine-DNA glycosylase; Provisional |
171 | pfam06093 | 77 | 23 | 27.2 | 26 | [ ---- ] | Spt4 | Spt4/RpoE2 zinc finger. This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery. |
172 | PRK13264 | 177 | 32 | 27.1 | 19 | [ ----- ] | PRK13264 | 3-hydroxyanthranilate 3,4-dioxygenase; Provisional |
173 | PRK12268 | 556 | 12 | 26.9 | 22 | [ - ] | PRK12268 | methionyl-tRNA synthetase; Reviewed |
174 | COG2176 | 1444 | 174 | 26.8 | 31 | [ ------------------------------] | PolC | DNA polymerase III, alpha subunit (gram-positive type) |
175 | pfam01873 | 125 | 29 | 26.7 | 25 | [ ---- ] | eIF-5_eIF-2B | Domain found in IF2B/IF5. This family includes the N terminus of eIF-5, and the C terminus of eIF-2 beta. This region corresponds to the whole of the archaebacterial eIF-2 beta homologue. The region contains a putative zinc binding C4 finger. |
176 | PRK07726 | 658 | 54 | 26.5 | 47 | [ --------- ] | PRK07726 | DNA topoisomerase III; Provisional |
177 | TIGR03269 | 520 | 25 | 26.1 | 27 | [ ---- ] | met_CoM_red_A2 | methyl coenzyme M reductase system, component A2. The enzyme that catalyzes the final step in methanogenesis, methyl coenzyme M reductase, contains alpha, beta, and gamma chains. In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed methyl coenzyme M reductase system component A2. |
178 | COG1198 | 730 | 30 | 26.1 | 31 | [ ----- ] | PriA | Primosomal protein N' (replication factor Y) - superfamily II helicase |
179 | COG3673 | 423 | 93 | 26.1 | 2.1E+02 | [ --------------- ] | COG3673 | Uncharacterized protein, PA2063/DUF2235 family |
180 | PRK08565 | 1103 | 28 | 25.9 | 29 | [ -----] | PRK08565 | DNA-directed RNA polymerase subunit B; Provisional |
181 | pfam12172 | 37 | 24 | 25.9 | 27 | [ ---- ] | DUF35_N | Rubredoxin-like zinc ribbon domain (DUF35_N). This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in Rv3521. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. |
182 | pfam00508 | 201 | 51 | 25.4 | 1.2E+02 | [ -------- ] | PPV_E2_N | E2 (early) protein, N terminal. |
183 | pfam14353 | 128 | 13 | 25.2 | 35 | [ - ] | CpXC | CpXC protein. This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea, and is typically between 122 and 134 amino acids in length. It contains four conserved cysteines forming two CpXC motifs. |
184 | PRK04000 | 411 | 39 | 24.9 | 39 | [ ------ ] | PRK04000 | translation initiation factor IF-2 subunit gamma; Validated |
185 | TIGR02889 | 435 | 86 | 24.9 | 32 | [ -------------- ] | spore_YpeB | germination protein YpeB. Members of this family are YpeB, a protein usually encoded with the putative spore-cortex-lytic enzyme SleB and required, together with SleB, for normal germination. This family is retricted to endospore-forming species in the Firmicutes lineage of bacteria, and found in all such species to date except Clostridium perfringens. The matching phenotypes of mutants in SleB (called a lytic transglycosylase) and YpeB suggests that YpeB is necessary to allow SleB to function. |
186 | COG3513 | 1088 | 35 | 24.8 | 3.1E+02 | [ ----- ] | Cas9 | CRISPR/Cas system Type II associated protein, contains McrA/HNH and RuvC-like nuclease domains |
187 | pfam00301 | 47 | 27 | 24.4 | 33 | [ ---- ] | Rubredoxin | Rubredoxin. |
188 | pfam10333 | 180 | 61 | 24.4 | 92 | [ --------- ] | Pga1 | GPI-Mannosyltransferase II co-activator. Pga1 is found only in yeasts and not in mammals. It localizes in the ER as a glycosylated integral membrane protein. It binds to the GPI-mannosyltransferase II subunit of the GPI and it is responsible for the second mannose addition to GPI precursors. The GPI-anchoring complex is a glycolipid that functions as a membrane anchor for many cell-surface proteins. |
189 | COG1675 | 176 | 29 | 24.4 | 17 | [ ---- ] | TFA1 | Transcription initiation factor IIE, alpha subunit |
190 | PRK14298 | 377 | 42 | 23.9 | 42 | [ ------- ] | PRK14298 | chaperone protein DnaJ; Provisional |
191 | pfam07503 | 34 | 24 | 23.8 | 30 | [ ---- ] | zf-HYPF | HypF finger. The HypF family of proteins are involved in the maturation and regulation of hydrogenase. In the N-terminus they appear to have two Zinc finger domains, as modelled by this family. |
192 | PRK00481 | 242 | 35 | 23.5 | 32 | [ -----] | PRK00481 | NAD-dependent deacetylase; Provisional |
193 | TIGR02827 | 595 | 52 | 23.3 | 65 | [ --------- ] | RNR_anaer_Bdell | anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons. |
194 | PRK08351 | 61 | 17 | 23.2 | 35 | [ --- ] | PRK08351 | DNA-directed RNA polymerase subunit E''; Validated |
195 | PRK05580 | 679 | 31 | 22.6 | 41 | [ ----- ] | PRK05580 | primosome assembly protein PriA; Validated |
196 | pfam01485 | 63 | 28 | 22.6 | 50 | [ ---- ] | IBR | IBR domain. The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease. |
197 | pfam01927 | 146 | 43 | 22.5 | 84 | [ ------- ] | Mut7-C | Mut7-C RNAse domain. RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C terminus. |
198 | pfam12738 | 63 | 48 | 21.7 | 70 | [ ---------- ] | PTCB-BRCT | twin BRCT domain. This is a BRCT domain that appears in duplicate in most member sequences. BRCT domains are peptide- and phosphopeptide-binding modules. BRCT domains are present in a number of proteins involved in DNA checkpoint controls and DNA repair. |
199 | PRK14811 | 269 | 30 | 21.4 | 35 | [ ---- ] | PRK14811 | formamidopyrimidine-DNA glycosylase; Provisional |
200 | PRK07111 | 735 | 40 | 21.3 | 40 | [ ------- ] | PRK07111 | anaerobic ribonucleoside triphosphate reductase; Provisional |
201 | PRK14701 | 1638 | 36 | 21.2 | 30 | [ ------] | PRK14701 | reverse gyrase; Provisional |
202 | pfam09334 | 388 | 47 | 21.1 | 18 | [ -------- ] | tRNA-synt_1g | tRNA synthetases class I (M). This family includes methionyl tRNA synthetases. |
203 | COG1552 | 50 | 28 | 21.0 | 33 | [ -----] | RPL40A | Ribosomal protein L40E |
204 | pfam08234 | 74 | 62 | 20.8 | 2.7E+02 | [ ---------- ] | Spindle_Spc25 | Chromosome segregation protein Spc25. This is a family of chromosome segregation proteins. It contains Spc25, which is a conserved eukaryotic kinetochore protein involved in cell division. In fungi the Spc25 protein is a subunit of the Nuf2-Ndc80 complex, and in vertebrates it forms part of the Ndc80 complex. |
205 | cd09394 | 55 | 19 | 20.6 | 61 | [ ---] | LIM1_Rga | The first LIM domain of Rga GTPase-Activating Proteins. The first LIM domain of Rga GTPase-Activating Proteins: The members of this family contain two tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Rga activates GTPases during polarized morphogenesis. In yeast, a known regulating target of Rga is CDC42p, a small GTPase. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. |
206 | PRK00750 | 510 | 40 | 20.5 | 46 | [ ------] | lysK | lysyl-tRNA synthetase; Reviewed |
207 | PRK05978 | 148 | 28 | 20.5 | 24 | [ ---- ] | PRK05978 | hypothetical protein; Provisional |
208 | cd07169 | 90 | 26 | 20.4 | 35 | [ ---- ] | NR_DBD_GCNF_like | DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). |
209 | pfam14577 | 235 | 17 | 20.4 | 35 | [ --- ] | SEO_C | Sieve element occlusion C-terminus. Sieve element occlusion (SEO) proteins, or forisomes, are phloem proteins which accumulate during sieve element differentiation. This domain represents the C-terminus of SEO proteins. |
210 | COG4049 | 65 | 13 | 20.4 | 40 | [ -- ] | COG4049 | Uncharacterized protein, contains archaeal-type C2H2 Zn-finger |
211 | PRK10445 | 263 | 27 | 20.3 | 51 | [ ---- ] | PRK10445 | endonuclease VIII; Provisional |
212 | COG3577 | 215 | 97 | 20.2 | 58 | [ ------------------- ] | COG3577 | Predicted aspartyl protease |