YRC Public Data Repository - Protein Structure Prediction

Protein:	pab-2
Organism:	Caenorhabditis elegans
Length:	692 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 pab-2.

Description	E-value	Query Range	Subject Range
gi\|73976805 - gi\|73976805\|ref\|XP_857859.1\| PREDICTED: similar to poly(A) binding protein, cytoplasmic 4 isoform 1 ...	507.0	[0..48]	[689..2]

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Predicted Domain #1

Region A:
Residues: [1-235]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAQVPPPMTQ VVTSAPPPTA AATVVAGAVA GQPQAVIQQG PPPTNIGYPP NATYSMASLY  60
   61 IGDLHPDVSE AMLFEKFSMA GPVLSIRVCR DNTSRLSLGY AYVNFQQPAD AERALDTMNF 120
  121 EVIHGRPMRI MWSQRDPAAR RAGNGNIFIK NLDRVIDNKS VYDTFSLFGN ILSCKVATDD 180
  181 EGNSKGYGFV HFETEHSAQT AIEKVNGMLL SDKKVYVGKF QPRAQRMKEL GESGL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	54.30103
Match:	1cvjA
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.73097473547076	bayes_pls_golite062009
	6.62953239642182	bayes_pls_golite062009
mRNA binding	5.29759606920196	bayes_pls_golite062009
nucleic acid binding	4.92126426323641	bayes_pls_golite062009
snRNA binding	4.06596327298973	bayes_pls_golite062009
binding	3.64400841800969	bayes_pls_golite062009
poly-pyrimidine tract binding	3.11990160533699	bayes_pls_golite062009
U1 snRNA binding	3.02511982045347	bayes_pls_golite062009
single-stranded RNA binding	2.93798024346416	bayes_pls_golite062009
poly(U) RNA binding	2.49013736906028	bayes_pls_golite062009
transcription regulator activity	2.18211199677674	bayes_pls_golite062009
protein binding	2.17260848225967	bayes_pls_golite062009
DNA binding	1.98418556946403	bayes_pls_golite062009
hydrolase activity	1.59923957614061	bayes_pls_golite062009
structural molecule activity	1.56454315220334	bayes_pls_golite062009
U2 snRNA binding	1.34078165372485	bayes_pls_golite062009
transcription factor activity	1.07843408116687	bayes_pls_golite062009
transcription repressor activity	1.06887262556449	bayes_pls_golite062009
mRNA 3'-UTR binding	0.824614388276642	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.632534695085793	bayes_pls_golite062009
eukaryotic initiation factor 4G binding	0.597542453741953	bayes_pls_golite062009
sequence-specific DNA binding	0.383589644462932	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	0.100880394187931	bayes_pls_golite062009
single-stranded DNA binding	0.0459458211377304	bayes_pls_golite062009
receptor binding	0.00911566774455674	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [236-329]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KYTNVFVKNF GEHLDQEKLS AMFSKFGEIT SAVVMTDAQG KPKGFGFVAF ADQDAAGQAV  60
   61 EKLNDSILEG TDCKLSVCRA QKKSERSAEL KRKY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	13.522879
Match:	1qm9A
Description:	Polypyrimidine tract-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.73097473547076	bayes_pls_golite062009
	6.62953239642182	bayes_pls_golite062009
mRNA binding	5.29759606920196	bayes_pls_golite062009
nucleic acid binding	4.92126426323641	bayes_pls_golite062009
snRNA binding	4.06596327298973	bayes_pls_golite062009
binding	3.64400841800969	bayes_pls_golite062009
poly-pyrimidine tract binding	3.11990160533699	bayes_pls_golite062009
U1 snRNA binding	3.02511982045347	bayes_pls_golite062009
single-stranded RNA binding	2.93798024346416	bayes_pls_golite062009
poly(U) RNA binding	2.49013736906028	bayes_pls_golite062009
transcription regulator activity	2.18211199677674	bayes_pls_golite062009
protein binding	2.17260848225967	bayes_pls_golite062009
DNA binding	1.98418556946403	bayes_pls_golite062009
hydrolase activity	1.59923957614061	bayes_pls_golite062009
structural molecule activity	1.56454315220334	bayes_pls_golite062009
U2 snRNA binding	1.34078165372485	bayes_pls_golite062009
transcription factor activity	1.07843408116687	bayes_pls_golite062009
transcription repressor activity	1.06887262556449	bayes_pls_golite062009
mRNA 3'-UTR binding	0.824614388276642	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.632534695085793	bayes_pls_golite062009
eukaryotic initiation factor 4G binding	0.597542453741953	bayes_pls_golite062009
sequence-specific DNA binding	0.383589644462932	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	0.100880394187931	bayes_pls_golite062009
single-stranded DNA binding	0.0459458211377304	bayes_pls_golite062009
receptor binding	0.00911566774455674	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [330-449]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EALKQERVQR YQGVNLYVKN IEEDLNDDGL RDHFSSFGTI TSAKVMVDEN GRSKGFGFVC  60
   61 FEKPEEATAA VTDMNSKMIG AKPLYVALAQ RKEDRRAQLA SQYMQRLATL RMGQQASGVP 120
  121

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	4.79
Match:	1u6fA
Description:	NMR solution structure of TcUBP1, a single RBD-unit from Trypanosoma cruzi
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
	6.40066880991253	bayes_pls_golite062009
RNA binding	6.32219487559982	bayes_pls_golite062009
mRNA binding	4.87640532914983	bayes_pls_golite062009
nucleic acid binding	4.65259034341669	bayes_pls_golite062009
snRNA binding	3.77997752511163	bayes_pls_golite062009
binding	3.48033873254013	bayes_pls_golite062009
U1 snRNA binding	2.73908382552928	bayes_pls_golite062009
poly-pyrimidine tract binding	2.7133834347239	bayes_pls_golite062009
single-stranded RNA binding	2.55628738360472	bayes_pls_golite062009
transcription regulator activity	2.2045206027152	bayes_pls_golite062009
poly(U) RNA binding	2.13305841145089	bayes_pls_golite062009
protein binding	2.10850948869511	bayes_pls_golite062009
DNA binding	1.99030664201171	bayes_pls_golite062009
hydrolase activity	1.62800695894716	bayes_pls_golite062009
structural molecule activity	1.57342338925793	bayes_pls_golite062009
transcription factor activity	1.09958329302628	bayes_pls_golite062009
U2 snRNA binding	1.09350203162237	bayes_pls_golite062009
transcription repressor activity	1.07516027015942	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.633093884585572	bayes_pls_golite062009
eukaryotic initiation factor 4G binding	0.468183942177665	bayes_pls_golite062009
mRNA 3'-UTR binding	0.462558743683805	bayes_pls_golite062009
sequence-specific DNA binding	0.327072171076297	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	0.0991482775217878	bayes_pls_golite062009
receptor binding	0.0174485064798613	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [450-614]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AMTQLYQPGQ QGYFVPNPMN AQGRPGFQPQ SAQIRGPPGQ RVFQNQMFMQ YPFNQRQVYP  60
   61 QQQGRPPMRT NDGRPQYGMA PRPAGAPRVG GPGVQMGGAP IRQQGPAPRG APQKPFYQGP 120
  121 PRQQQPQQHS QQPAQQPGQQ GQGQSGIVIH GQETLTSHML AQAAP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.154902
Match:	1m2vB
Description:	Sec24
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [615-692]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QEQKQLLGER IYALIEKMFP NHKEAGKITG MMLEIDNAEL IMMLQDAELF RSKVEEAFGV  60
   61 LTNAQSAAAS TSAPTAKN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	29.221849
Match:	1g9lA
Description:	poly(A) binding protein
Matching Structure (courtesy of the PDB):

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:

Predicted functions:

Predicted functions: