YRC Public Data Repository - Protein Structure Prediction

Protein:	MRM1
Organism:	Saccharomyces cerevisiae
Length:	412 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for MRM1.

Description	E-value	Query Range	Subject Range
MRM1 - Ribose methyltransferase that modifies a functionally critical, conserved nucleotide in mitochondria... MRM1_YEAST - rRNA methyltransferase 1, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=...	0.0	[1..412]	[1..412]
gi\|6523570, gi\|2... - gi\|6523570\|emb\|CAB62290.1\| hypothetical protein [Zygosaccharomyces rouxii], gi\|238940563\|emb\|CAR2873... gi\|254584204 - gi\|254584204\|ref\|XP_002497670.1\| ZYRO0F10868p [Zygosaccharomyces rouxii]	5.0E-76	[28..410]	[34..411]
gi\|7469455 - pir\|\|S76163 hypothetical protein - Synechocystis sp. (strain PCC 6803) Y955_SYNY3 - Uncharacterized tRNA/rRNA methyltransferase slr0955 OS=Synechocystis sp. (strain ATCC 27184 / PCC 68... Y955_SYNY3 - Uncharacterized tRNA/rRNA methyltransferase slr0955 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) ...	4.0E-67	[16..412]	[34..364]
gi\|237703847, gi... - gi\|237703847\|ref\|ZP_04534328.1\| RNA methyltransferase [Escherichia sp. 3_2_53FAA], gi\|226901759\|gb\|E... gi\|227836350, gi... - gi\|227886777\|ref\|ZP_04004582.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli 83972... gi\|115515650, gi... - gi\|117626526\|ref\|YP_859849.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli APEC O1... gi\|124528239, gi... - gi\|124528239\|ref\|ZP_01699563.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli B], gi... gi\|75234271, gi\|... - gi\|75234271\|ref\|ZP_00718659.1\| COG0566: rRNA methylases [Escherichia coli E110019], gi\|193070849\|ref... gi\|191170707, gi... - gi\|75242430\|ref\|ZP_00726192.1\| COG0566: rRNA methylases [Escherichia coli F11], gi\|75236167\|ref\|ZP_0... gi\|75212271, gi\|... - gi\|75212271\|ref\|ZP_00712311.1\| COG0566: rRNA methylases [Escherichia coli B171], gi\|194426679\|ref\|ZP... gi\|190904353, gi... - gi\|75231227\|ref\|ZP_00717634.1\| COG0566: rRNA methylases [Escherichia coli B7A], gi\|191165658\|ref\|ZP_... gi\|73858142, gi\|... - gi\|74314665\|ref\|YP_313084.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Shigella sonnei Ss046], g... gi\|89110900, gi\|... - gi\|89110900\|ref\|AP_004680.1\| 23S rRNA (Gm2251)-methyltransferase [Escherichia coli str. K-12 substr.... gi\|192926325, gi... - gi\|75255907\|ref\|ZP_00727639.1\| COG0566: rRNA methylases [Escherichia coli E22], gi\|193066002\|ref\|ZP_... gi\|188489607, gi... - gi\|75515419\|ref\|ZP_00737576.1\| COG0566: rRNA methylases [Escherichia coli 53638], gi\|188494408\|ref\|Z... gi\|157080504, gi... - gi\|75188891\|ref\|ZP_00702158.1\| COG0566: rRNA methylases [Escherichia coli E24377A], gi\|157158474\|ref... gi\|75198026, gi\|... - gi\|75198026\|ref\|ZP_00708096.1\| COG0566: rRNA methylases [Escherichia coli HS], gi\|157163645\|ref\|YP_0... gi\|83585082, gi\|... - gi\|83585082\|ref\|ZP_00923735.1\| COG0566: rRNA methylases [Escherichia coli 101-1], gi\|194439536\|ref\|Z... gi\|254796199, gi... - gi\|254796199\|ref\|YP_003081036.1\| 23S rRNA (Gm2251)-methyltransferase [Escherichia coli O157:H7 str. ... gi\|254164109, gi... - gi\|254164109\|ref\|YP_003047217.1\| 23S rRNA (Gm2251)-methyltransferase [Escherichia coli B str. REL606... gi\|254037194, gi... - gi\|254037194\|ref\|ZP_04871271.1\| 23S rRNA-methyltransferase [Escherichia sp. 1_1_43], gi\|226840300\|gb... gi\|253775195, gi... - gi\|254290859\|ref\|YP_003056607.1\| 23S rRNA (Gm2251)-methyltransferase [Escherichia coli BL21(DE3)], g... gi\|251787429, gi... - gi\|251787429\|ref\|YP_003001733.1\| hypothetical protein B21_04009 [Escherichia coli BL21], gi\|24237970... gi\|238859752, gi... - gi\|238903287\|ref\|YP_002929083.1\| 23S rRNA (Gm2251)-methyltransferase [Escherichia coli BW2952], gi\|2... gi\|215489524, gi... - gi\|215489524\|ref\|YP_002331955.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli O127... gi\|217326510, gi... - gi\|217326510\|ref\|ZP_03442594.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H... gi\|218358992, gi... - gi\|218551450\|ref\|YP_002385242.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia fergusoni... gi\|218363501, gi... - gi\|218556732\|ref\|YP_002389646.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli IAI1... gi\|218561339, gi... - gi\|218561339\|ref\|YP_002394252.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli S88]... gi\|218430078, gi... - gi\|218692514\|ref\|YP_002400726.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli ED1a... gi\|218354661, gi... - gi\|218697929\|ref\|YP_002405596.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli 5598... gi\|218372863, gi... - gi\|218702877\|ref\|YP_002410506.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli IAI3... gi\|169891461, gi... - gi\|170083626\|ref\|YP_001732946.1\| 23S rRNA (Gm2251)-methyltransferase [Escherichia coli str. K-12 sub... gi\|170517295, gi... - gi\|170679577\|ref\|YP_001746575.1\| RNA methyltransferase [Escherichia coli SMS-3-5], gi\|170517295\|gb\|A... gi\|194417170, gi... - gi\|194434585\|ref\|ZP_03066842.1\| RNA methyltransferase, TrmH family, group 3 [Shigella dysenteriae 10... gi\|195935970 - gi\|195935970\|ref\|ZP_03081352.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli O157:... gi\|208726719, gi... - gi\|208806918\|ref\|ZP_03249255.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H... gi\|208813496, gi... - gi\|208813496\|ref\|ZP_03254825.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H... gi\|208818601, gi... - gi\|208818601\|ref\|ZP_03258921.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H... gi\|209160633, gi... - gi\|209399233\|ref\|YP_002273722.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:... gi\|24054863, gi\|... - gi\|24115535\|ref\|NP_710045.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Shigella flexneri 2a str.... RLMB_ECOL6 - 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 70... RLMB_ECO57 - 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB OS=Escherichia coli O157:H7 GN=rlmB PE=3 SV=1 gi\|30065552, gi\|... - gi\|30065552\|ref\|NP_839723.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Shigella flexneri 2a str.... RLMB_ECOL6 - 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB OS=Escherichia coli O6 GN=rlmB PE=3 SV=1 EG12483 - 23S rRNA mG2251 2'-O-ribose methyltransferase, SAM-dependent / 23S rRNA mG2251 2'-O-ribose methyltra... RLMB_ECOLI - 23S rRNA (guanosine-2'-O-)-methyltransferase rlmB (EC 2.1.1.-) (23S rRNA Gm2251 2'-O-methyltransfera... gi\|15804769, gi\|... - gi\|15804769\|ref\|NP_290810.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli O157:H7 ... gi\|218434888, gi... - gi\|218707791\|ref\|YP_002415310.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli UMN0... RLMB_SHIFL - 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB OS=Shigella flexneri GN=rlmB PE=3 SV=1 EG12483 - 23S rRNA mG2251 2'-O-ribose methyltransferase, SAM-dependent / 23S rRNA mG2251 2'-O-ribose methyltra... gi\|91213729, gi\|... - gi\|91213729\|ref\|YP_543715.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli UTI89], ... gi\|189357886, gi... - gi\|189357886\|gb\|EDU76305.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H7 st... gi\|13364633, gi\|... - gi\|15834410\|ref\|NP_313183.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli O157:H7 ... gi\|189368907, gi... - gi\|189368907\|gb\|EDU87323.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H7 st... gi\|110644537, gi... - gi\|110644537\|ref\|YP_672267.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli 536], g... gi\|168766459, gi... - gi\|189364243\|gb\|EDU82662.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H7 st... gi\|110808098, gi... - gi\|110808098\|ref\|YP_691618.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Shigella flexneri 5 str.... gi\|187770173, gi... - gi\|187770173\|gb\|EDU34017.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H7 st... gi\|189001755, gi... - gi\|189001755\|gb\|EDU70741.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H7 st... gi\|189374953, gi... - gi\|189374953\|gb\|EDU93369.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H7 st... gi\|168801835, gi... - gi\|189376090\|gb\|EDU94506.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H7 st... gi\|170021810, gi... - gi\|170021810\|ref\|YP_001726764.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Escherichia coli ATCC... gi\|168751468, gi... - gi\|188014500\|gb\|EDU52622.1\| RNA methyltransferase, TrmH family, group 3 [Escherichia coli O157:H7 st...	3.0E-62	[122..412]	[1..242]
gi\|62130448, gi\|... - gi\|62182815\|ref\|YP_219232.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica subsp... gi\|56416160, gi\|... - gi\|56416160\|ref\|YP_153235.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica subsp... gi\|238910527 - gi\|238910527\|ref\|ZP_04654364.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica su... RLMB_SALTY - 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB OS=Salmonella typhimurium (strain LT2 / SGSC1412 /... lcl\|NC_016856.1_... - [gene=yjfH] [protein=23S rRNA (guanosine-2'-O-)-methyltransferase] [protein_id=YP_005240682.1] [loca... gi\|197365085, gi... - gi\|197365085\|ref\|YP_002144722.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica s... gi\|204927331, gi... - gi\|204927331\|ref\|ZP_03218533.1\| RNA methyltransferase, TrmH family, group 3 [Salmonella enterica sub... gi\|213428664 - gi\|213428664\|ref\|ZP_03361414.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica su... gi\|213582911 - gi\|213582911\|ref\|ZP_03364737.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica su... gi\|194449058, gi... - gi\|194449058\|ref\|YP_002048412.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica s... gi\|194469123, gi... - gi\|194469123\|ref\|ZP_03075107.1\| RNA methyltransferase, TrmH family, group 3 [Salmonella enterica sub... RLMB_SALTY - 23S rRNA (guanosine-2'-O-)-methyltransferase rlmB OS=Salmonella typhimurium GN=rlmB PE=3 SV=1 gi\|194734163, gi... - gi\|194734163\|ref\|YP_002117310.1\| RNA methyltransferase, TrmH family, group 3 [Salmonella enterica su... gi\|197263055, gi... - gi\|197263055\|ref\|ZP_03163129.1\| RNA methyltransferase, TrmH family, group 3 [Salmonella enterica sub... gi\|197287651, gi... - gi\|197287651\|gb\|EDY27042.1\| RNA methyltransferase, TrmH family, group 3 [Salmonella enterica subsp. ... gi\|205336077, gi... - gi\|205336077\|gb\|EDZ22841.1\| RNA methyltransferase, TrmH family, group 3 [Salmonella enterica subsp. ... gi\|205341078, gi... - gi\|205341078\|gb\|EDZ27842.1\| RNA methyltransferase, TrmH family, group 3 [Salmonella enterica subsp. ... gi\|194444737, gi... - gi\|194444737\|ref\|YP_002043624.1\| RNA methyltransferase, TrmH family, group 3 [Salmonella enterica su... gi\|161617640, gi... - gi\|161617640\|ref\|YP_001591605.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica s... gi\|205327237, gi... - gi\|205327237\|gb\|EDZ14001.1\| RNA methyltransferase, TrmH family, group 3 [Salmonella enterica subsp. ... RLMB_SALTY - 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB OS=Salmonella typhimurium GN=rlmB PE=3 SV=1 gi\|168231407, gi... - gi\|205334208\|gb\|EDZ20972.1\| RNA methyltransferase, TrmH family, group 3 [Salmonella enterica subsp. ... gi\|213852966 - gi\|213852966\|ref\|ZP_03382498.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica su... gi\|214003352 - gi\|214003352\|ref\|ZP_03414087.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica su... gi\|224586209, gi... - gi\|224586209\|ref\|YP_002640008.1\| putative tRNA/rRNA methyltransferase [Salmonella enterica subsp. en...	1.0E-61	[122..412]	[1..242]
gi\|213021981 - gi\|213021981\|ref\|ZP_03336428.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica su... RLMB_SALTI - 23S rRNA (guanosine-2'-O-)-methyltransferase rlmB OS=Salmonella typhi GN=rlmB PE=3 SV=1 gi\|29140306, gi\|... - gi\|29144667\|ref\|NP_808009.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica subsp... RLMB_SALTI - 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB OS=Salmonella typhi GN=rlmB PE=3 SV=1 gi\|16763188 - gi\|16763188\|ref\|NP_458805.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica subsp... gi\|213648977 - gi\|213648977\|ref\|ZP_03379030.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica su... gi\|213417716 - gi\|213417716\|ref\|ZP_03350838.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Salmonella enterica su...	6.0E-61	[122..412]	[1..242]
gi\|25316695 - pir\|\|A83664 tRNA/rRNA methyltransferase BH0113 [imported] - Bacillus halodurans (strain C-125) gi\|15612676, gi\|... - gi\|15612676\|ref\|NP_240979.1\| tRNA/rRNA methyltransferase [Bacillus halodurans C-125], gi\|10172725\|db...	5.0E-60	[123..412]	[3..243]
RLMB_PASMU - 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB OS=Pasteurella multocida (strain Pm70) GN=rlmB PE=... RLMB_PASMU - 23S rRNA (guanosine-2'-O-)-methyltransferase rlmB OS=Pasteurella multocida GN=rlmB PE=3 SV=1	2.0E-59	[122..412]	[1..243]
gi\|25325048 - pir\|\|AD1951 tRNA/rRNA methyltransferase [imported] - Nostoc sp. (strain PCC 7120) gi\|17130505, gi\|... - gi\|17228654\|ref\|NP_485202.1\| tRNA/rRNA methyltransferase [Nostoc sp. PCC 7120], gi\|17130505\|dbj\|BAB7...	2.0E-59	[45..412]	[4..321]
gi\|18146090, gi\|... - gi\|18311406\|ref\|NP_563340.1\| RNA methyltransferase, TrmH family, group 3 [Clostridium perfringens st... gi\|182626981, gi... - gi\|182626981\|ref\|ZP_02954711.1\| RNA methyltransferase, TrmH family, group 3 [Clostridium perfringens... gi\|168214713, gi... - gi\|170713821\|gb\|EDT26003.1\| RNA methyltransferase, TrmH family, group 3 [Clostridium perfringens CPE...	6.0E-59	[51..412]	[2..286]

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Predicted Domain #1

Region A:
Residues: [1-85]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTSLTNAVFK RYLAVTPSAH QALKTRIKKK SSSFDKFFPQ QSNSRKKQWE TLNEDKASWF  60
   61 KRKYAHVHAR EQDRAADPYG KKKAH

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.388	0.109	rRNA modification	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.237	0.011	rRNA modification	a.24.17	Group V grass pollen allergen
View	Download	0.368	0.009	rRNA modification	a.46.1	Methionine synthase domain
View	Download	0.337	0.008	rRNA modification	a.181.1	Antibiotic binding domain of TipA-like multidrug resistance regulators
View	Download	0.388	N/A	N/A	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.368	N/A	N/A	a.46.1	Methionine synthase domain
View	Download	0.337	N/A	N/A	a.181.1	Antibiotic binding domain of TipA-like multidrug resistance regulators
View	Download	0.237	N/A	N/A	a.24.17	Group V grass pollen allergen

Predicted Domain #2

Region A:
Residues: [86-230]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VEKLKEIKNQ AKLNQKSHKS KFQNKDIALK LMNDNPIFEY VYGTNSVYAA LLNPSRNCHS  60
   61 RLLYHGTIPS KFLQIVDELK VTTELVDKHR LNLLTNYGVH NNIALETKPL QPVEIAYLGD 120
  121 MDTSSAALSI HELGFNNENI PHELP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.39794
Match:	1ipaA_
Description:	RrmH, C-terminal domain; RrmH, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA methyltransferase activity	4.23455016472464	bayes_pls_golite062009
methyltransferase activity	3.59960278169345	bayes_pls_golite062009
transferase activity, transferring one-carbon groups	3.51722801996622	bayes_pls_golite062009
rRNA methyltransferase activity	3.14976989427746	bayes_pls_golite062009
tRNA methyltransferase activity	2.33123191403389	bayes_pls_golite062009
S-adenosylmethionine-dependent methyltransferase activity	2.23755555119187	bayes_pls_golite062009
tRNA (guanine) methyltransferase activity	2.14623472760939	bayes_pls_golite062009
transferase activity	1.63934797352054	bayes_pls_golite062009
structural constituent of ribosome	1.0137045454994	bayes_pls_golite062009
catalytic activity	0.797300463760338	bayes_pls_golite062009
N-methyltransferase activity	0.736216022000293	bayes_pls_golite062009
structural molecule activity	0.694233763389628	bayes_pls_golite062009
binding	0.650146274744039	bayes_pls_golite062009
nucleic acid binding	0.404179021204849	bayes_pls_golite062009
rRNA (guanine) methyltransferase activity	0.319046095835882	bayes_pls_golite062009
	0.16936231012632	bayes_pls_golite062009
snoRNA binding	0.155192244522672	bayes_pls_golite062009
protein binding	0.031057919963412	bayes_pls_golite062009
rRNA (guanine-N1-)-methyltransferase activity	6.26422903788337E-4	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [231-412]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YGTKTDAKKF PLGLYLDEIT DPHNIGAIIR SAYFLGVDFI VMSRRNCSPL TPVVSKTSSG  60
   61 ALELLPIFYV DKPLEFFTKS QEMGGWTFIT SHLANATSEK YTVGKTISMH DLNGLCNELP 120
  121 VVLVVGNESQ GVRTNLKMRS DFFVEIPFGG IEKGNRAPEP IVDSLNVSVA TALLIDNILT 180
  181 CK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.39794
Match:	1ipaA_
Description:	RrmH, C-terminal domain; RrmH, N-terminal domain
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: