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