YRC Public Data Repository - Protein Structure Prediction

Protein:	RBM39_PONPY
Organism:	Pongo pygmaeus
Length:	524 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 RBM39_PONPY.

Description	E-value	Query Range	Subject Range
gi\|61557287, gi\|... - gi\|61557287\|ref\|NP_001013225.1\| RNA binding motif protein 39 [Rattus norvegicus], gi\|60552170\|gb\|AAH... gi\|74196119, gi\|... - gi\|74196119\|dbj\|BAE32977.1\| unnamed protein product [Mus musculus], gi\|220872598\|emb\|CAX15275.1\| RNA...	1.0E-61	[1..524]	[1..524]
gi\|73991848 - gi\|73991848\|ref\|XP_865304.1\| PREDICTED: similar to RNA-binding region containing protein 2 isoform b...	3.0E-61	[1..524]	[1..527]
gi\|76633420 - gi\|76633420\|ref\|XP_886666.1\| PREDICTED: similar to RNA-binding region containing protein 2 isoform b...	3.0E-61	[1..524]	[1..525]
IPI:IPI00555302.... - Ensembl_locations(Chr-bp):3-139264164, Tax_Id=10116 RNA-binding region, Tax_Id=10116 RNA-binding reg... RBM39_MOUSE - RNA-binding protein 39 OS=Mus musculus GN=Rbm39 PE=1 SV=2	4.0E-60	[1..524]	[1..530]
gi\|166831598 - gi\|166831598\|gb\|ABY90123.1\| RNA binding motif protein 39 isoform a (predicted) [Callithrix jacchus] gi\|73991844, gi\|... - gi\|73991850\|ref\|XP_865323.1\| PREDICTED: similar to RNA-binding region containing protein 2 (Hepatoce... gi\|76633408 - gi\|76633408\|ref\|XP_873382.1\| PREDICTED: RNA binding motif protein 39 isoform 2 [Bos taurus] gi\|169731519 - gi\|169731519\|gb\|ACA64891.1\| RNA binding motif protein 39 isoform a (predicted) [Callicebus moloch] gi\|229368730 - gi\|229368730\|gb\|ACQ63013.1\| RNA binding motif protein 39 isoform a (predicted) [Dasypus novemcinctus... RBM39 - RNA binding motif protein 39 gi\|149733225 - gi\|149733225\|ref\|XP_001501869.1\| PREDICTED: RNA binding motif protein 39 isoform 1 [Equus caballus] gi\|197215647 - gi\|197215647\|gb\|ACH53039.1\| RNA binding motif protein 39 isoform a (predicted) [Otolemur garnettii] gi\|194044531 - gi\|194044531\|ref\|XP_001925257.1\| PREDICTED: RNA binding motif protein 39 isoform 1 [Sus scrofa] gi\|164623752 - gi\|164623752\|gb\|ABY64678.1\| RNA binding motif protein 39, isoform 1 (predicted) [Papio anubis] gi\|217038339 - gi\|217038339\|gb\|ACJ76632.1\| RNA binding motif protein 39 isoform a (predicted) [Oryctolagus cuniculu...	5.0E-60	[1..524]	[1..530]

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Predicted Domain #1

Region A:
Residues: [1-237]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MADDIDIEAM LEAPYKKDEN KLSSANGHEE RSKKRKKSKS RSRSHERKRS KSKERKRSRD  60
   61 RERKKSKSRE RKRSRSKERR RSRSRSRDRR FRGRYRSPYS GPKFNSAIRG KIGLPHSIKL 120
  121 SRRRSRSKSP FRKDKSPVRE PIDNLTPEER DARTVFCMQL AARIRPRDLE EFFSTVGKVR 180
  181 DVRMISDRNS RRSKGIAYVE FVDVSSVPLA IGLTGQRVLG VPIIVQASQA EKNRAAA

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	6.26
Match:	1l3kA
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
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
binding	3.48033873254013	bayes_pls_golite062009
snRNA binding	2.99850361909067	bayes_pls_golite062009
poly-pyrimidine tract binding	2.7133834347239	bayes_pls_golite062009
single-stranded RNA binding	2.55628738360472	bayes_pls_golite062009
U1 snRNA binding	1.97699928565988	bayes_pls_golite062009
transcription regulator activity	1.94691250607537	bayes_pls_golite062009
DNA binding	1.80828042019548	bayes_pls_golite062009
structural molecule activity	1.30816853575581	bayes_pls_golite062009
transcription factor activity	1.17242427495624	bayes_pls_golite062009
protein binding	1.05805521997665	bayes_pls_golite062009
sequence-specific DNA binding	0.327072171076297	bayes_pls_golite062009
mRNA 3'-UTR binding	0.229644510503376	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [238-342]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MANNLQKGSA GPMRLYVGSL HFNITEDMLR GIFEPFGRIE SIQLMMDSET GRSKGYGFIT  60
   61 FSDSECAKKA LEQLNGFELA GRPMKVGHVT ERTDASSASS FLDSD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11.522879
Match:	2cq4A
Description:	solution structure of RNA binding domain in RNA binding motif protein 23
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [343-416]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ELERTGIDLG TTGRLQLMAR LAEGTGLQIP PAAQQALQMS GSLAFGAVAD LQTRLSQQTE  60
   61 ASALAAAASV QPLA

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #4

Region A:
Residues: [417-524]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TQCFQLSNMF NPQTEEEVGW DTEIKDDVIE ECNKHGGVIH IYVDKNSAQG NVYVKCPSIA  60
   61 AAIAAVNALH GRWFAGKMIT AAYVPLPTYH NLFPDSMTAT QLLVPSRR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	5.39794
Match:	1whxA
Description:	Solution structure of the second RNA binding domain from hypothetical protein BAB23448
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
binding	3.64400841800969	bayes_pls_golite062009
snRNA binding	3.28448936696877	bayes_pls_golite062009
poly-pyrimidine tract binding	3.11990160533699	bayes_pls_golite062009
single-stranded RNA binding	2.93798024346416	bayes_pls_golite062009
U1 snRNA binding	2.26303528058407	bayes_pls_golite062009
transcription regulator activity	1.92450390013691	bayes_pls_golite062009
DNA binding	1.8021593476478	bayes_pls_golite062009
structural molecule activity	1.29928829870122	bayes_pls_golite062009
transcription factor activity	1.15127506309683	bayes_pls_golite062009
protein binding	1.12215421354121	bayes_pls_golite062009
mRNA 3'-UTR binding	0.591700155096213	bayes_pls_golite062009
sequence-specific DNA binding	0.383589644462932	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:

Predicted functions: