YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|214035392, gi...
Organism:	Carboxydibrachium pacificum DSM 12653
Length:	236 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|214035392, gi....

Description	E-value	Query Range	Subject Range
gi\|166854456, gi... - gi\|167040216\|ref\|YP_001663201.1\| pseudouridine synthase [Thermoanaerobacter sp. X514], gi\|166854456\|... gi\|242231811, gi... - gi\|242256647\|ref\|ZP_04801534.1\| pseudouridine synthase [Thermoanaerobacter sp. X513], gi\|242231811\|g... gi\|241902757, gi... - gi\|241902757\|ref\|ZP_04787488.1\| pseudouridine synthase [Thermoanaerobacter brockii subsp. finnii Ako... gi\|167037554, gi... - gi\|76796400\|ref\|ZP_00778763.1\| Pseudouridine synthase, Rsu [Thermoanaerobacter ethanolicus ATCC 3322...	234.0	[0..1]	[236..1]
gi\|196252016, gi... - gi\|196252016\|ref\|ZP_03150680.1\| pseudouridine synthase [Clostridium thermocellum DSM 4150], gi\|19619... gi\|125713436, gi... - gi\|67917292\|ref\|ZP_00510945.1\| Pseudouridine synthase, Rsu [Clostridium thermocellum ATCC 27405], gi...	227.0	[0..2]	[230..4]
gi\|39983385, gi\|... - gi\|39996504\|ref\|NP_952455.1\| ribosomal large subunit pseudouridine synthase B [Geobacter sulfurreduc...	225.0	[0..3]	[233..4]
gi\|158140808, gi... - gi\|158320609\|ref\|YP_001513116.1\| pseudouridine synthase [Alkaliphilus oremlandii OhILAs], gi\|1581408...	225.0	[0..2]	[235..1]
gi\|27262400 - gi\|27262400\|gb\|AAN87481.1\| Ribosomal large subunit pseudouridine synthase B [Heliobacillus mobilis]	225.0	[0..3]	[234..12]
gi\|255307056 - gi\|255307056\|ref\|ZP_05351227.1\| putative 23S RNA and tRNA pseudouridine synthase [Clostridium diffic... gi\|115251104, gi... - gi\|126699667\|ref\|YP_001088564.1\| putative 23S RNA and tRNA pseudouridine synthase [Clostridium diffi... gi\|255101182 - gi\|255101182\|ref\|ZP_05330159.1\| putative 23S RNA and tRNA pseudouridine synthase [Clostridium diffic...	222.0	[0..2]	[236..1]
gi\|15024828, gi\|... - gi\|15895126\|ref\|NP_348475.1\| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824], gi\|1502... gi\|25323995 - pir\|\|D97128 probable pseudouridylate synthase [imported] - Clostridium acetobutylicum	222.0	[0..3]	[235..4]
gi\|220931567, gi... - gi\|89211767\|ref\|ZP_01190111.1\| Pseudouridine synthase, Rsu [Halothermothrix orenii H 168], gi\|891586...	221.0	[0..1]	[236..1]
gi\|134051705, gi... - gi\|88945031\|ref\|ZP_01148252.1\| Pseudouridine synthase, Rsu [Desulfotomaculum reducens MI-1], gi\|8892...	221.0	[0..3]	[235..4]
gi\|255517442 - gi\|255517442\|ref\|ZP_05385118.1\| putative 23S RNA and tRNA pseudouridine synthase [Clostridium diffic... gi\|255650552 - gi\|255650552\|ref\|ZP_05397454.1\| putative 23S RNA and tRNA pseudouridine synthase [Clostridium diffic... gi\|90574437, gi\|... - gi\|90574437\|ref\|ZP_01230937.1\| hypothetical protein CdifQ_02002193 [Clostridium difficile QCD-32g58]... gi\|254975638 - gi\|254975638\|ref\|ZP_05272110.1\| putative 23S RNA and tRNA pseudouridine synthase [Clostridium diffic... gi\|255093025 - gi\|255093025\|ref\|ZP_05322503.1\| putative 23S RNA and tRNA pseudouridine synthase [Clostridium diffic... gi\|255314767 - gi\|255314767\|ref\|ZP_05356350.1\| putative 23S RNA and tRNA pseudouridine synthase [Clostridium diffic...	220.0	[0..2]	[236..1]

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Predicted Domain #1

Region A:
Residues: [1-236]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVRLQKYLAE CGIASRRKCE EYILQGRVKV NGKVVKELGT KIDPDVDIIE FDDKIVRREE  60
   61 KKVYIMLYKP AGYITSVKDP FGRPTVLDLV KVKERIYPVG RLDFDTSGLL LLTNDGELAN 120
  121 ILMHPKHEIV KTYVAKIKGI PTKEEMERFE NGLIIDGRKT AKAKIRILNV KNGTSVVEIQ 180
  181 IHEGRNRQVK KMCKAIGHPV IALKRTKIGE LELKGLKPGE WRYLTEDEIR YLKSLR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	47.522879
Match:	1kskA
Description:	Ribosomal small subunit pseudouridine 516 synthase RsuA; Pseudouridine synthase RsuA N-terminal domain
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
structural constituent of ribosome	1.93805098366683	bayes_pls_golite062009
structural molecule activity	1.65902435754631	bayes_pls_golite062009
RNA binding	0.351909066993469	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: