YRC Public Data Repository - Protein Structure Prediction

Protein:	RLMD_SHEON
Organism:	Shewanella oneidensis MR-1
Length:	449 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 RLMD_SHEON.

Description	E-value	Query Range	Subject Range
gi\|114046682, gi... - gi\|78691673\|ref\|ZP_00856276.1\| 23S rRNA methyltransferase/RumA [Shewanella sp. MR-7], gi\|78508925\|gb...	363.0	[0..1]	[449..15]
RLMD_SHESA - 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD OS=Shewanella sp. (strain ANA-3) GN=rlmD PE=3 SV...	362.0	[0..1]	[449..1]
gi\|113969454, gi... - gi\|82497521\|ref\|ZP_00883054.1\| 23S rRNA methyltransferase/RumA [Shewanella sp. MR-4], gi\|82404444\|gb...	361.0	[0..1]	[449..15]
gi\|46113357, gi\|... - gi\|68054113\|ref\|ZP_00538277.1\| 23S rRNA methyltransferase/RumA [Exiguobacterium sibiricum 255-15], g...	353.0	[0..10]	[449..1]
RLMD_SHESW - 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD OS=Shewanella sp. (strain W3-18-1) GN=rlmD PE=3 ...	351.0	[0..1]	[446..1]
gi\|226224354, gi... - gi\|226224354\|ref\|YP_002758461.1\| hypothetical RNA methyltransferase [Listeria monocytogenes Clip8145... gi\|254992256 - gi\|254992256\|ref\|ZP_05274446.1\| hypothetical RNA methyltransferase [Listeria monocytogenes FSL J2-06... Y1776_LISMF - Uncharacterized RNA methyltransferase LMOf2365_1776 OS=Listeria monocytogenes serotype 4b (strain F2...	351.0	[0..13]	[446..6]
RLMD_SHEPC - 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD OS=Shewanella putrefaciens (strain CN-32 / ATCC ...	351.0	[0..1]	[446..1]
YEFA_BACSU, RLMC... - Uncharacterized RNA methyltransferase yefA OS=Bacillus subtilis GN=yefA PE=3 SV=1, 23S rRNA (uracil-... gi\|221312833 - gi\|221312833\|ref\|ZP_03594638.1\| hypothetical protein BsubsN3_03754 [Bacillus subtilis subsp. subtili... RLMCD_BACSU - 23S rRNA (uracil-C(5))-methyltransferase RlmCD OS=Bacillus subtilis (strain 168) GN=rlmCD PE=1 SV=1 gi\|221317757 - gi\|221317757\|ref\|ZP_03599051.1\| hypothetical protein BsubsJ_03708 [Bacillus subtilis subsp. subtilis... gi\|221322036 - gi\|221322036\|ref\|ZP_03603330.1\| hypothetical protein BsubsS_03794 [Bacillus subtilis subsp. subtilis...	350.0	[0..7]	[449..1]
RLMD_SHEB9 - 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD OS=Shewanella baltica (strain OS195) GN=rlmD PE=...	350.0	[0..1]	[446..1]
Y1863_LISIN - Uncharacterized RNA methyltransferase lin1863 OS=Listeria innocua serovar 6a (strain CLIP 11262) GN=... Y1863_LISIN, YI6... - (Q92AQ7) Hypothetical RNA methyltransferase lin1863 (EC 2.1.1.-), Uncharacterized RNA methyltransfer...	349.0	[0..13]	[448..6]

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Predicted Domain #1

Region A:
Residues: [1-449]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAQFFKAKPN SSKQLSAKQS FSVQQLDHLG AGIAQHQGKV VFIPGALPNE TVQAQLTEQK  60
   61 KNYARAKLIK VETPSTERVS PLCPHYHTCG GCDLQHMSLT AQREHKSAAL VDIMAKFAGA 120
  121 EGSLAPALSG EGWHYRRRAR LATLFDKNTK QLSLGFRASS SSHVVSITEC LVLAKPLSDL 180
  181 IAPFAKLLNQ LAAKSSLGHL ELIAADNGHF AVIRITKSLN DKDMAKLAQF AEQHQIHICL 240
  241 QDNEGEFHGV NGTLLLPVYQ LLDDKTDVQP VSLTFTPGNF VQVNAQINKA MVAQALDWLA 300
  301 PQPGERILDL FCGMGNFSLP LARMGADVIG VEGVPEMVSQ ARENAVANGL SNLTFYHGDL 360
  361 SADLSSEPWM GKIDKLLLDP ARAGAYESLQ WLKKMKPRQV VYVSCNPASL ARDSAVLLER 420
  421 GYKLQKLGLI DMFPQTHHIE AMALFELAK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	87.522879
Match:	1uwvA
Description:	Crystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA 5-Methyluridine Methyltransferase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
methyltransferase activity	4.64500705012502	bayes_pls_golite062009
rRNA methyltransferase activity	4.60300178039953	bayes_pls_golite062009
transferase activity, transferring one-carbon groups	4.57389022626587	bayes_pls_golite062009
S-adenosylmethionine-dependent methyltransferase activity	3.74830027382001	bayes_pls_golite062009
RNA methyltransferase activity	3.6174490060285	bayes_pls_golite062009
N-methyltransferase activity	3.00112136063228	bayes_pls_golite062009
protein methyltransferase activity	2.74535979387581	bayes_pls_golite062009
transferase activity	2.42370637689376	bayes_pls_golite062009
tRNA methyltransferase activity	2.15176183511624	bayes_pls_golite062009
rRNA (adenine) methyltransferase activity	2.03602074114015	bayes_pls_golite062009
rRNA (adenine-N6,N6-)-dimethyltransferase activity	1.93015827477588	bayes_pls_golite062009
DNA-methyltransferase activity	1.8182614465692	bayes_pls_golite062009
catalytic activity	1.62377578202456	bayes_pls_golite062009
histone methyltransferase activity	1.42140847541194	bayes_pls_golite062009
arginine N-methyltransferase activity	1.40233857644962	bayes_pls_golite062009
protein-arginine N-methyltransferase activity	1.40233857644962	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	1.35012187932492	bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds	1.35012187932492	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	1.34692777988167	bayes_pls_golite062009
rRNA (guanine) methyltransferase activity	1.26573118969035	bayes_pls_golite062009
site-specific DNA-methyltransferase (adenine-specific) activity	0.88654745691593	bayes_pls_golite062009
histone-arginine N-methyltransferase activity	0.67380437956274	bayes_pls_golite062009
ligase activity	0.616411670715755	bayes_pls_golite062009
O-methyltransferase activity	0.59365370184158	bayes_pls_golite062009
rRNA (guanine-N2-)-methyltransferase activity	0.427131446117391	bayes_pls_golite062009
protein-arginine omega-N monomethyltransferase activity	0.355464145533041	bayes_pls_golite062009
tRNA (guanine) methyltransferase activity	0.355378060639199	bayes_pls_golite062009
rRNA (cytosine) methyltransferase activity	0.346042596102079	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: