YRC Public Data Repository - Protein Structure Prediction

Protein:	nam9
Organism:	Schizosaccharomyces pombe
Length:	327 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 nam9.

Description	E-value	Query Range	Subject Range
gi\|11282525, gi\|... - gi\|1749714\|dbj\|BAA13914.1\| unnamed protein product [Schizosaccharomyces pombe], gi\|11282525\|pir\|\|T43...	207.0	[0..1]	[327..1]
gi\|39983385, gi\|... - gi\|39996504\|ref\|NP_952455.1\| ribosomal large subunit pseudouridine synthase B [Geobacter sulfurreduc...	194.0	[0..94]	[314..1]
gi\|27262400 - gi\|27262400\|gb\|AAN87481.1\| Ribosomal large subunit pseudouridine synthase B [Heliobacillus mobilis]	188.0	[0..88]	[319..3]
RR4_OENHO - Chloroplast 30S ribosomal protein S4 - Oenothera hookeri (Hooker's evening primrose)	183.0	[0..4]	[205..3]
gi\|78193687, gi\|... - gi\|78222432\|ref\|YP_384179.1\| ribosomal large subunit pseudouridine synthase B [Geobacter metalliredu...	182.0	[0..94]	[314..1]
gi\|51856610, gi\|... - gi\|51892921\|ref\|YP_075612.1\| ribosomal large subunit pseudouridine synthase B [Symbiobacterium therm...	182.0	[0..94]	[318..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...	182.0	[0..95]	[314..3]
RR4_EUCGG - 30S ribosomal protein S4, chloroplastic OS=Eucalyptus globulus subsp. globulus GN=rps4 PE=3 SV=1	181.0	[0..4]	[203..3]
gi\|29422405 - gi\|29422405\|gb\|AAO84598.1\| small ribosomal protein 4 [Breutelia chrysocoma]	181.0	[0..5]	[203..2]
RR4_LEUSC - 30S ribosomal protein S4, chloroplastic OS=Leucodon sciuroides GN=rps4 PE=3 SV=1	181.0	[0..4]	[203..3]

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Predicted Domain #1

Region A:
Residues: [1-83]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKGKFRFSLK RGLLRPSWNK YNIYNIARKQ LPALNNRTLY QKKWNAKKET RSYHGPQLRE  60
   61 YQLKNAFRPK LEGVISSLDN KLP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	39.69897
Match:	2uu9D
Description:	No description for 2uu9D was found.

Predicted Domain #2

Region A:
Residues: [84-327]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IPFMNQTYAF LESRLDMSIH RALFASSALQ ARQLVLHGKV HVNGKPERRA YRQLLPGDLV  60
   61 TVDQKSVMNC VSASSNNTPS IQDGKQTEQV SSKDGENEKK KDNDDDLFEQ TSNGKLPSIN 120
  121 ETISNFVPKP FMSLMAFIPA YLEVCFRTCS FVYVRDPVAR PGLTEVPSPF PEDLHALAYT 180
  181 YYIRSRNMRQ GAARCQARRL IPQKVRDASF YQGPPELYKK RNVSPKEAFS HRYPVRQGKL 240
  241 TKLV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	38.0
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
structural constituent of ribosome	9.39690558966302	bayes_pls_golite062009
structural molecule activity	8.82127733244958	bayes_pls_golite062009
catalytic activity	2.02180970970004	bayes_pls_golite062009
RNA binding	1.78858120096157	bayes_pls_golite062009
pseudouridine synthase activity	1.78394310345744	bayes_pls_golite062009
isomerase activity	1.03309280368247	bayes_pls_golite062009
nucleic acid binding	0.926923419656671	bayes_pls_golite062009
binding	0.803280718980961	bayes_pls_golite062009
intramolecular transferase activity	0.67639306881958	bayes_pls_golite062009
transcription regulator activity	0.372664455687289	bayes_pls_golite062009
DNA binding	0.210201731988272	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: