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 is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

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: