match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	cd07957	129	58	72.9	22	[       ----------------------------------------  ]	Anticodon_Ia_Met	Anticodon-binding domain of methionyl tRNA synthetases. This domain is found in methionyl tRNA synthetases (MetRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon (CAU). MetRS catalyzes the transfer of methionine to the 3'-end of its tRNA.
2	pfam11125	54	39	66.9	9.2	[    ------------------------                     ]	DUF2830	Protein of unknown function (DUF2830). Several members in this viral family of proteins are annotated as lysis proteins.
3	cd14424	37	25	60.9	4.8	[                              --------------     ]	CUE_Cue1p_like	CUE domain found in yeast ubiquitin-binding protein CUE1 (Cue1p), CUE4 (Cue4p) and similar proteins. Cue1p, also called coupling of ubiquitin conjugation to ER degradation protein 1 or kinetochore-defect suppressor 4, is encoded by the open reading frame (ORF) YMR264W in yeast. It is an N-terminally membrane-anchored endoplasmic reticulum (ER) protein essential for the activity of the two major yeast RING finger ubiquitin ligases (E3s) implicated in ER-associated degradation (ERAD). It interacts with the ERAD ubiquitin-conjugating enzyme (E2) Ubc7p in vivo, stimulates Ubc7p E2 activity, and further activates ER-associated protein degradation. Cue1p contains a CUE domain which binds ubiquitin much more weakly than those of other CUE domain containing proteins. It also has an Ubc7p binding-domain at the C-terminal region which is required for Ubc7p-dependent ubiquitylation and for degradation of substrates in the ER. This family also includes Cue4p, also called coupling of ubiquitin conjugation to ER degradation protein 4. It is encoded by the open reading frame (ORF) YML101C in yeast. Cue4p contains a CUE domain which shows high level of similarity with that of Cue1p.
4	cd05592	320	21	58.2	4.5	[                                ------------     ]	STKc_nPKC_theta_like	Catalytic domain of the Serine/Threonine Kinases, Novel Protein Kinase C theta, delta, and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKC-theta is selectively expressed in T-cells and plays an important and non-redundant role in several aspects of T-cell biology. PKC-delta plays a role in cell cycle regulation and programmed cell death in many cell types. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. There are four nPKC isoforms, delta, epsilon, eta, and theta. The nPKC-theta-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.
5	pfam04100	375	61	56.4	34	[   -----------------------------------------     ]	Vps53_N	Vps53-like, N-terminal. Vps53 complexes with Vps52 and Vps54 to form a multi- subunit complex involved in regulating membrane trafficking events.
6	TIGR02552	135	29	55.5	4.2	[                          ----------------       ]	LcrH_SycD	type III secretion low calcium response chaperone LcrH/SycD. Genes in this family are found in type III secretion operons. LcrH, from Yersinia is believed to have a regulatory function in the low-calcium response of the secretion system. The same protein is also known as SycD (SYC = Specific Yop Chaperone) for its chaperone role. In Pseudomonas, where the homolog is known as PcrH, the chaperone role has been demonstrated and the regulatory role appears to be absent. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
7	pfam14559	68	28	50.3	33	[                              ----------------   ]	TPR_19	Tetratricopeptide repeat.
8	cd00215	97	20	49.7	14	[                                    ------------ ]	PTS_IIA_lac	PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation.
9	pfam07719	34	15	46.9	23	[                                    --------     ]	TPR_2	Tetratricopeptide repeat. This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by pfam00515.
10	pfam13428	44	20	46.2	23	[                                  -----------    ]	TPR_14	Tetratricopeptide repeat.
11	pfam02845	42	33	45.5	11	[                          -------------------    ]	CUE	CUE domain. CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2.
12	pfam01471	57	32	43.0	46	[       ------------------                        ]	PG_binding_1	Putative peptidoglycan binding domain. This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.
13	cd02186	434	15	42.9	13	[                                     --------    ]	alpha_tubulin	The alpha-tubulin family. The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. The alpha/beta-tubulin heterodimer is the structural subunit of microtubules. The alpha- and beta-tubulins share 40% amino-acid sequence identity, exist in several isotype forms, and undergo a variety of posttranslational modifications. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three regions based on function: the amino-terminal nucleotide-binding region, an intermediate taxol-binding region and the carboxy-terminal region which probably constitutes the binding surface for motor proteins.
14	PRK14110	291	34	38.1	28	[   -----------------------                       ]	PRK14110	F0F1 ATP synthase subunit gamma; Provisional
15	COG1447	105	22	37.9	28	[                                    ------------ ]	CelC	Phosphotransferase system cellobiose-specific component IIA
16	pfam07721	26	15	37.8	31	[                                   ---------     ]	TPR_4	Tetratricopeptide repeat. This Pfam entry includes tetratricopeptide-like repeats not detected by the pfam00515, pfam07719 and pfam07720 models.
17	cd05578	257	21	36.6	18	[                                ------------     ]	STKc_Yank1	Catalytic domain of the Serine/Threonine Kinase, Yank1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily contains uncharacterized STKs with similarity to the human protein designated as Yank1 or STK32A. The Yank1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.
18	pfam11577	68	16	36.4	21	[                                      ---------  ]	NEMO	NF-kappa-B essential modulator NEMO. NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini.The core domain of NEMO is a dimer which binds to two fragments of IKK.
19	COG4273	135	37	36.4	21	[         ---------------------                   ]	COG4273	Uncharacterized protein, contains metal-binding DGC domain
20	pfam00231	288	33	35.2	36	[    ----------------------                       ]	ATP-synt	ATP synthase.
21	pfam13181	34	19	34.2	42	[                                  -----------    ]	TPR_8	Tetratricopeptide repeat.
22	pfam05991	165	19	33.7	29	[                                     ----------- ]	NYN_YacP	YacP-like NYN domain. This family consists of bacterial proteins related to YacP. This family is uncharacterized functionally, but it has been suggested that these proteins are nucleases due to them containing a NYN domain. NYN (for N4BP1, YacP-like Nuclease) domains were discovered by Anantharaman and Aravind. Based on gene neighborhoods it was suggested that the bacterial YacP proteins interact with the Ribonuclease III and TrmH methylase in a processome complex that catalyzes the maturation of rRNA and tRNA.
23	pfam05068	169	59	33.2	63	[           -----------------------------------   ]	MtlR	Mannitol repressor. The mannitol operon of Escherichia coli, encoding the mannitol-specific enzyme II of the phosphotransferase system (MtlA) and mannitol phosphate dehydrogenase (MtlD) contains an additional downstream open reading frame which encodes the mannitol repressor (MtlR).
24	pfam10769	74	37	32.9	84	[        ---------------------                    ]	DUF2594	Protein of unknown function (DUF2594). This family of proteins with unknown function appear to be restricted to Enterobacteriaceae.
25	cd14368	41	23	32.4	37	[                               -------------     ]	CUE_DEF1_like	CUE domain found in fungal RNA polymerase II degradation factor 1 (DEF1) and similar proteins. DEF1, also called RRM3-interacting protein 1, is a RNA Polymerase II (RNAPII) degradation factor that may be required to couple arrested RNAPII to the proteasome to facilitate its degradation. It contains a CUE domain that is responsible for the binding of ubiquitin. The family also includes many uncharacterized hypothetical proteins. They show a high level of sequence similarity with DEF1.
26	cd12151	282	32	32.4	36	[    ---------------------                        ]	F1-ATPase_gamma	mitochondrial ATP synthase gamma subunit. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain of F-ATPases is composed of alpha, beta, gamma, delta, and epsilon (not present in bacteria) subunits with a stoichiometry of 3:3:1:1:1. Alpha and beta subunit form the globular catalytic moiety, a hexameric ring of alternating subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton translocating domain.
27	TIGR03029	274	35	32.3	34	[    ----------------------                       ]	EpsG	chain length determinant protein tyrosine kinase EpsG. The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF).
28	pfam14804	52	29	32.1	16	[                     ------------------          ]	Jag_N	Jag N-terminus. This domain is found at the N-terminus of proteins containing pfam13083 and pfam01424, including the jag proteins.
29	pfam02255	96	21	31.9	40	[                                    ------------ ]	PTS_IIA	PTS system, Lactose/Cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIA PTS system enzymes. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation.
30	PRK10613	74	35	29.8	1E+02	[        ---------------------                    ]	PRK10613	hypothetical protein; Provisional
31	PRK00133	673	62	29.4	3.1E+02	[    ------------------------------------------   ]	metG	methionyl-tRNA synthetase; Reviewed
32	pfam06202	367	19	28.8	52	[                                    -----------  ]	GDE_C	Amylo-alpha-1,6-glucosidase. This family includes human glycogen branching enzyme. This enzyme contains a number of distinct catalytic activities. It has been shown for the yeast homologue that mutations in this region disrupt the enzymes Amylo-alpha-1,6-glucosidase (EC:3.2.1.33).
33	PRK14562	204	18	28.8	40	[                                      ---------- ]	PRK14562	haloacid dehalogenase superfamily protein; Provisional
34	pfam14561	90	27	28.7	53	[                              ---------------    ]	TPR_20	Tetratricopeptide repeat.
35	PRK13423	288	34	28.2	48	[   -----------------------                       ]	PRK13423	F0F1 ATP synthase subunit gamma; Provisional
36	pfam12178	38	27	27.8	71	[                     ---------------             ]	INCENP_N	Chromosome passenger complex (CPC) protein INCENP N terminal. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. INCENP is a regulatory protein in the chromosome passenger complex. It is involved in regulation of the catalytic protein Aurora B. It performs this function in association with two other proteins - Survivin and Borealin. These proteins form a tight three-helical bundle. The N terminal domain is the domain involved in formation of this three helical bundle.
37	cd09525	67	31	27.6	42	[ ---------------------                           ]	SAM_GAREM	SAM domain of GAREM subfamily. SAM (sterile alpha motif) domain of GAREM (Grb2-associated and regulator of Erk/MARK) protein subfamily (also known as FAM59A) is a putative protein-protein interaction domain. SAM domain is a widespread domain in signaling proteins. Proteins of this group have SAM at the C-terminus. Human GAREM protein is known to play a role in regulation of the EGF (Epidermal Growth Factor) receptor and of Gab or insulin preceptor substrate-1 family proteins. Grb2 (Growth factor receptor-bound) protein was identified as a binding partner of human GAREM. Proline-rich motifs and phosphorylation of two conserved tyrosines in GAREM are important for the interaction with the SH3 domains of Grb2 protein; however these motifs and residues do not belong to the SAM domain.
38	cd14484	134	48	27.3	2E+02	[    ----------------------------                 ]	SPX_GDE1_like	SPX domain of Gde1 and similar proteins. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family. The yeast protein Gde1/Ypl110c is similar to both, NUC-2 and Pho81, in sharing their multi-domain architecture, which includes the SPX N-terminal domain followed by several ankyrin repeats and a C-terminal glycerophosphodiester phosphodiesterase domain (GDPD). Gde1 hydrolyzes intracellular glycerophosphocholine into glycerolphosphate and choline, and plays a role in the utilization of glycerophosphocholine as a source for phosphate.
39	pfam14048	96	16	26.7	37	[                                    ---------    ]	MBD_C	C-terminal domain of methyl-CpG binding protein 2 and 3. CpG-methylation is a frequently occurring epigenetic modification of vertebrate genomes resulting in transcriptional repression. This domain was found at the C-terminus of the methyl-CpG-binding domain (MBD) containing proteins MBD2 and MBD3, the latter was shown to not bind directly to methyl-CpG DNA but rather interact with components of the NuRD/Mi2 complex, an abundant deacetylase complex. The domain is subject to structure determination by the Joint Center of Structural Genomics.
40	PRK14994	287	45	26.3	92	[    ----------------------------------           ]	PRK14994	SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional
41	TIGR01935	150	44	26.0	10	[      ---------------------------------          ]	NOT-MenG	RraA famliy. The E. coli member of this family has been characterized as a regulator of RNase E and its crystal structure has been analyzed. This model was initially classified as a "hypothetical equivalog" expressing the tentative hypothesis that all members might have the same function as the E. coli enzyme. Considering the second clade of enterobacterial sequences within this family, that appears to be less tenable. The function of these sequences outside of the narrow RraA equivalog model (TIGR02998) remains obscure. All of these were initially annotated as MenG, AKA S-adenosylmethionine: 2-demethylmenaquinone methyltransferase (EC 2.1.-.-). See the references characterizing this as a case of transitive annotation error in the case of the E. coli protein.
42	pfam08542	89	13	25.4	57	[                                      -------    ]	Rep_fac_C	Replication factor C C-terminal domain. This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A.
43	TIGR01146	286	34	25.3	55	[   -----------------------                       ]	ATPsyn_F1gamma	ATP synthase, F1 gamma subunit. This model describes the ATP synthase gamma subunit in bacteria and its equivalents in organelles, namely, mitochondria and chloroplast. F1/F0-ATP synthase is a multisubunit, membrane associated enzyme found in bacteria and organelles of higher eukaryotes, namely, mitochondria and chloroplast. This enzyme is principally involed in the synthesis of ATP from ADP and inorganic phosphate by coupling the energy derived from the proton electrochemical gradient across the biological membrane. A brief description of this multisubunit enzyme complex: F1 and F0 represent two major clusters of subunits. The gamma subunit is the part of F1 cluster. Surrounding the gamma subunit in a cylinder-like structure are three alpha and three subunits in an alternating fashion. This is the central catalytic unit whose different conformations permit the binding of ADP and inorganic phosphate and release of ATP.
44	pfam13374	42	16	25.2	75	[                                   ---------     ]	TPR_10	Tetratricopeptide repeat.
45	pfam12752	57	17	25.0	40	[                                   ---------     ]	SUZ	SUZ domain. The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterized in the C.elegans protein Szy-20 where it has been shown to bind RNA and allow their localization to the centrosome. Warning- the domain has a compositionally biased character.
46	pfam09537	111	38	24.7	1.9E+02	[  ----------------------                         ]	DUF2383	Domain of unknown function (DUF2383). Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown.
47	pfam08859	110	29	24.6	20	[          -----------------                      ]	DGC	DGC domain. This domain appears to be a zinc binding domain from the conservation of four potential chelating cysteines. The domain is named after a conserved central motif. The function of this domain is unknown.
48	PRK06253	529	10	23.9	30	[          ------                                 ]	PRK06253	O-phosphoseryl-tRNA synthetase; Reviewed
49	pfam06957	421	22	23.6	51	[                                 ------------    ]	COPI_C	Coatomer (COPI) alpha subunit C-terminus. This family represents the C-terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit. Coatomer (COPI) is a large cytosolic protein complex which forms a coat around vesicles budding from the Golgi apparatus. Such coatomer-coated vesicles have been proposed to play a role in many distinct steps of intracellular transport. Note that many family members also contain the pfam04053 domain.
50	pfam10056	86	24	23.2	1E+02	[                                   --------------]	DUF2293	Uncharacterized conserved protein (DUF2293). This domain, found in various hypothetical bacterial proteins, has no known function.
51	TIGR00756	35	18	23.0	83	[                                   ----------    ]	PPR	pentatricopeptide repeat domain (PPR motif). This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
52	cd01000	228	30	22.5	99	[                   -------------------------     ]	PBP2_Cys_DEBP_like	Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 periplasmic-binding protein fold. This family comprises of the periplasmic-binding protein component of ABC transporters specific for cysteine and carboxylic amino acids, as well as their closely related proteins. The cysteine and aspartate-glutamate binding domains belong to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.
53	pfam04533	212	49	22.4	1.9E+02	[  ----------------------------                   ]	Herpes_U44	Herpes virus U44 protein. This is a family of proteins from dsDNA beta-herpesvirinae and gamma-herpesvirinae viruses. The function is not known, and the proteins are named variously as U44, BSRF1, UL71, and M71. The family BSRF1 has been merged into this.
54	cd14820	182	17	21.7	82	[                                       --------- ]	TRAX	Translin-associated factor-X (TRAX). TRAX (translin-associated factor-X) is a paralog of its binding partner protein Translin and together they form oligomeric complexes known as C3PO proteins (for component 3 promoter of RNA-induced silencing complex or RISC). TRAX complexed with Translin is possibly involved in dendritic RNA processing and in DNA double-strand break repair as an interacting partner with C1D, an activator of the DNA-dependent protein kinase involved in the repair of DNA-double strand breaks. It has been shown that Trax subunit, but not Translin, possesses a Glu-Glu-Asp catalytic center with the capacity to digest RNA; this catalytic activity is required for passenger-strand removal and RISC activation in RNAi. In Archaeoglobus fulgidus, Trax-like-subunits assemble into an octameric structure, highly similar to human C3PO; its complex with duplex RNA reveals that the octamer entirely encapsulates a single 13-base-pair RNA duplex inside a large inner cavity. Translin and Trax participate in a variety of nucleic acid metabolism pathways in addition to RNAi and have been implicated in a wide range of biological activities, including mRNA processing, cell growth regulation, spermatogenesis, neuronal development/function, genome stability regulation and carcinogenesis; however, their precise role in some of the processes remains unclear.
55	pfam01900	104	31	21.4	21	[           ------------------                    ]	RNase_P_Rpp14	Rpp14/Pop5 family. tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule associated with at least eight protein subunits, hPop1, Rpp14, Rpp20, Rpp25, Rpp29, Rpp30, Rpp38, and Rpp40. This protein is known as Pop5 in eukaryotes.
56	COG3275	557	74	21.0	3.6E+02	[   --------------------------------------------- ]	LytS	Sensor histidine kinase, LytS/YehU family
57	TIGR03158	357	38	20.9	24	[              ----------------------             ]	cas3_cyano	CRISPR-associated helicase Cas3, subtype CYANO. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.
58	PRK00440	319	17	20.5	81	[                                     ----------  ]	rfc	replication factor C small subunit; Reviewed
59	PRK03717	120	9	20.4	40	[                        -----                    ]	PRK03717	ribonuclease P protein component 2; Provisional
60	COG5023	443	16	20.3	58	[                                    ---------    ]	COG5023	Tubulin
61	cd10155	82	22	20.2	81	[ -------------                                   ]	BsYrkD-like_DUF156	Uncharacterized protein YrkD from Bacillus subtilis and related domains; this domain superfamily was previously known as part of DUF156. This domain family contains an uncharacterized protein YrkD from Bacillus subtilis and related proteins. This family is part of a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily. In this family, however, not all these residues are conserved, there is an Asn instead of the His (C-N-C); also a conserved Tyr and a Glu residue that facilitates allosteric regulation of DNA binding for CsoRs are very poorly conserved.