YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|2136190, gi\|1...
Organism:	Homo sapiens
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 gi|2136190, gi|1....

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 are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

Found no 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: