YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|16411297, gi\|...
Organism:	Listeria monocytogenes
Length:	303 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|16411297, gi|....

Description	E-value	Query Range	Subject Range
gi\|254931987 - gi\|254931987\|ref\|ZP_05265346.1\| hypothetical protein LmonH_06137 [Listeria monocytogenes HPB2262] gi\|254878039 - gi\|254878039\|ref\|ZP_05250749.1\| hypothetical protein LmonFSL_02517 [Listeria monocytogenes FSL J2-07... gi\|46908075, gi\|... - gi\|46908075\|ref\|YP_014464.1\| ribosomal large subunit pseudouridine synthase D [Listeria monocytogene... gi\|47094208, gi\|... - gi\|47094208\|ref\|ZP_00231922.1\| ribosomal large subunit pseudouridine synthase, RluD subfamily [Liste... gi\|133726785, gi... - gi\|153167686\|ref\|ZP_01927790.1\| hypothetical protein LMHG_00612 [Listeria monocytogenes FSL N1-017],... gi\|226224446, gi... - gi\|226224446\|ref\|YP_002758553.1\| hypothetical protein Lm4b_01859 [Listeria monocytogenes Clip81459],... gi\|254852749 - gi\|254852749\|ref\|ZP_05242097.1\| hypothetical protein LmonoFSL_05426 [Listeria monocytogenes FSL R2-5... gi\|254826115 - gi\|254826115\|ref\|ZP_05231116.1\| hypothetical protein LmonFS_13146 [Listeria monocytogenes FSL J1-194...	307.0	[0..1]	[303..1]
gi\|20807974, gi\|... - gi\|20807974\|ref\|NP_623145.1\| pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter tengcong... gi\|20807974 - gi\|20807974\|ref\|NP_623145.1\| Pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter tengcong...	306.0	[0..9]	[302..12]
gi\|221322942 - gi\|221322942\|ref\|ZP_03604236.1\| hypothetical protein BsubsS_08522 [Bacillus subtilis subsp. subtilis... gi\|221318669 - gi\|221318669\|ref\|ZP_03599963.1\| hypothetical protein BsubsJ_08416 [Bacillus subtilis subsp. subtilis... gi\|221313745 - gi\|221313745\|ref\|ZP_03595550.1\| hypothetical protein BsubsN3_08482 [Bacillus subtilis subsp. subtili... YLYB_BACSU - Uncharacterized RNA pseudouridine synthase YlyB OS=Bacillus subtilis (strain 168) GN=ylyB PE=3 SV=3 YLYB_BACSU - Uncharacterized RNA pseudouridine synthase ylyB OS=Bacillus subtilis GN=ylyB PE=3 SV=3	306.0	[0..1]	[301..1]
gi\|16414458, gi\|... - pir\|\|AC1677 conserved hypothetical protein homolog lin1957 [imported] - Listeria innocua (strain Cli... gi\|16801023 - gi\|16801023\|ref\|NP_471291.1\| hypothetical protein lin1957 [Listeria innocua Clip11262]	305.0	[0..1]	[301..1]
gi\|32468746, gi\|... - gi\|50812225\|ref\|NP_389429.2\| hypothetical protein BSU15460 [Bacillus subtilis subsp. subtilis str. 1... YLYB_BACSU - Uncharacterized RNA pseudouridine synthase ylyB OS=Bacillus subtilis GN=ylyB PE=3 SV=2	304.0	[0..1]	[301..1]
gi\|229330881, gi... - gi\|229498191\|ref\|ZP_04391888.1\| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC52], gi\|2... gi\|56379523, gi\|... - gi\|56419681\|ref\|YP_146999.1\| hypothetical protein GK1146 [Geobacillus kaustophilus HTA426], gi\|56379... gi\|221087579, gi... - gi\|221087579\|ref\|ZP_03557116.1\| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC61], gi\|2...	304.0	[0..1]	[302..1]
gi\|76587739, gi\|... - gi\|76796894\|ref\|ZP_00779243.1\| Pseudouridine synthase, RluD [Thermoanaerobacter ethanolicus ATCC 332...	303.0	[0..9]	[299..13]
gi\|116627406, gi... - gi\|62527693\|ref\|ZP_00388963.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Streptococcus t...	301.0	[0..6]	[300..1]
gi\|253753476, gi... - gi\|253753476\|ref\|YP_003026617.1\| RNA pseudouridylate synthase [Streptococcus suis P1/7], gi\|25181972... gi\|253751575, gi... - gi\|253751575\|ref\|YP_003024716.1\| putative RNA pseudouridylate synthase [Streptococcus suis SC84], gi... gi\|223934286, gi... - gi\|223934286\|ref\|ZP_03626210.1\| pseudouridine synthase, RluA family [Streptococcus suis 89/1591], gi... gi\|31364860 - gi\|31364860\|gb\|AAP49462.1\| YlyB [Streptococcus suis] gi\|251818162, gi... - gi\|253755698\|ref\|YP_003028838.1\| RNA pseudouridylate synthase [Streptococcus suis BM407], gi\|2518181...	300.0	[0..6]	[302..1]
gi\|114843803, gi... - gi\|114843803\|ref\|ZP_01454263.1\| Pseudouridine synthase, RluD [Thermoanaerobacter ethanolicus X514], ...	300.0	[0..9]	[299..13]

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Predicted Domain #1

Region A:
Residues: [1-303]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MQNETLIIEE SHARERVDKV IAEMMGKSRS AIQLMLKNGD ITVNGELAKP NYKVQVGDEI  60
   61 HYEVREPEEL EVLAEDIPLD IYFEDKDMLV VNKPEGMVVH PSAGHASGTL VNALLFHCDD 120
  121 LSGINGKIRP GIVHRIDKDT SGLLMVAKND HAHESLAKQL KDKTSDREYI ALVHGDIVHQ 180
  181 KGTIEAPIGR AKEDRQKMAV VRDGKEARTH FEVLERLPGY TLINCKLDTG RTHQIRVHLK 240
  241 YIGHPLAGDP KYGPKNTIKG NGQFLHAAKL GFDHPTTNER MTFEAPLPSS FEKALKSLRQ 300
  301 EEY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	69.39794
Match:	1qyuA
Description:	Structure of the catalytic domain of 23S rRNA pseudouridine synthase RluD
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
pseudouridine synthase activity	5.60483019625575	bayes_pls_golite062009
intramolecular transferase activity	4.62815459483632	bayes_pls_golite062009
isomerase activity	3.43067391737824	bayes_pls_golite062009
catalytic activity	2.39224964671205	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: