YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|213648977
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. J185
Length:	243 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 gi|213648977.

Description	E-value	Query Range	Subject Range
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...	2.0E-72	[1..243]	[1..243]
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-72	[1..243]	[1..243]
gi\|81247990, gi\|... - gi\|82546579\|ref\|YP_410526.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Shigella boydii Sb227], g...	6.0E-72	[1..243]	[1..243]
gi\|81243586, gi\|... - gi\|82779438\|ref\|YP_405787.1\| 23S rRNA (guanosine-2'-O-)-methyltransferase [Shigella dysenteriae Sd19...	1.0E-71	[1..243]	[1..243]
RLMB_PHOLL - 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB OS=Photorhabdus luminescens subsp. laumondii (stra... RLMB_PHOLL - 23S rRNA (guanosine-2'-O-)-methyltransferase rlmB OS=Photorhabdus luminescens subsp. laumondii GN=rl...	2.0E-71	[1..243]	[1..243]
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...	3.0E-71	[3..242]	[4..243]
gi\|187427311, gi... - gi\|75179449\|ref\|ZP_00699453.1\| COG0566: rRNA methylases [Shigella boydii BS512], gi\|187730319\|ref\|YP...	4.0E-71	[1..243]	[1..243]
gi\|106895728, gi... - gi\|158319524\|ref\|YP_001512031.1\| RNA methyltransferase [Alkaliphilus oremlandii OhILAs], gi\|15813972...	2.0E-69	[1..243]	[1..244]
gi\|238787548, gi... - gi\|77973971\|ref\|ZP_00829514.1\| COG0566: rRNA methylases [Yersinia frederiksenii ATCC 33641], gi\|2387...	4.0E-69	[1..242]	[1..242]
gi\|77954715, gi\|... - gi\|77954715\|ref\|ZP_00819103.1\| RNA methyltransferase TrmH, group 3 [Marinobacter aquaeolei VT8], gi\|...	5.0E-69	[2..242]	[3..243]

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Predicted Domain #1

Region A:
Residues: [1-243]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSEMIYGIHA VQALLERAPE RFQEAFILKG REDKRLLPLI HALESQGVVI QLANRQYLDE  60
   61 KSDGAVHQGI IARVKPGRQY QENDLPDLIA LHDRPFLLIL DGVTDPHNLG ACLRSADAAG 120
  121 VHAVIVPKDR SAQLNATAKK VACGAAESVP LIRVTNLART MRMLQEENIW IVGTAGEADH 180
  181 TLYQSKMPGR MALVMGAEGE GMRRLTREHC DELISIPMAG SVSSLNVSVA TGICLFEAVR 240
  241 QRT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	74.0
Match:	1gz0A
Description:	RlmB, C-terminal domain; RlmB, 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
RNA binding	2.61675538965988	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
nucleic acid binding	1.81000672982144	bayes_pls_golite062009
transferase activity	1.63934797352054	bayes_pls_golite062009
binding	1.31970199852267	bayes_pls_golite062009
structural constituent of ribosome	1.0137045454994	bayes_pls_golite062009
N-methyltransferase activity	0.736216022000293	bayes_pls_golite062009
structural molecule activity	0.694233763389628	bayes_pls_golite062009
rRNA (guanine) methyltransferase activity	0.319046095835882	bayes_pls_golite062009
catalytic activity	0.264002643439785	bayes_pls_golite062009
	0.16936231012632	bayes_pls_golite062009
snoRNA binding	0.155192244522672	bayes_pls_golite062009
protein binding	0.131685221037103	bayes_pls_golite062009
rRNA (guanine-N1-)-methyltransferase activity	6.26422903788337E-4	bayes_pls_golite062009

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: