YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|61359622, gi\|...
Organism:	synthetic construct
Length:	467 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|61359622, gi|....

Description	E-value	Query Range	Subject Range
gi\|1333645 - gi\|1333645\|gb\|AAB39329.1\| Mad2 gene product	0.0	[1..467]	[1..467]
gi\|58332038, gi\|... - gi\|58332038\|ref\|NP_001011168.1\| SMAD family member 2 [Xenopus (Silurana) tropicalis], gi\|54648024\|gb...	0.0	[1..467]	[1..467]
SMAD2_MOUSE - Mothers against decapentaplegic homolog 2 OS=Mus musculus GN=Smad2 PE=1 SV=2 gi\|117616710 - gi\|117616710\|gb\|ABK42373.1\| Smad2 [synthetic construct]	0.0	[1..467]	[1..467]
gi\|61369683, gi\|... - gi\|61369683\|gb\|AAX43373.1\| SMAD mothers against DPP-like 2 [synthetic construct], gi\|32880105\|gb\|AAP...	0.0	[1..467]	[1..467]
SMAD2_RAT - Mothers against decapentaplegic homolog 2 OS=Rattus norvegicus GN=Smad2 PE=1 SV=1	0.0	[1..467]	[1..467]
gi\|17384013, gi\|... - gi\|46048929\|ref\|NP_989892.1\| Sma- and Mad-related protein 2 [Gallus gallus], gi\|17384013\|emb\|CAC8540...	0.0	[1..467]	[1..467]
SMAD2_PONAB - Mothers against decapentaplegic homolog 2 OS=Pongo abelii GN=SMAD2 PE=2 SV=1 SMAD2_PONPY - Mothers against decapentaplegic homolog 2 - Pongo pygmaeus (Orangutan)	0.0	[1..467]	[1..467]
SMAD2_BOVIN - Mothers against decapentaplegic homolog 2 OS=Bos taurus GN=SMAD2 PE=2 SV=1	0.0	[1..467]	[1..467]

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Predicted Domain #1

Region A:
Residues: [1-174]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSSILPFTPP VVKRLLGWKK SAGGSGGAGG GEQNGQEEKW CEKAVKSLVK KLKKTGRLDE  60
   61 LEKAITTQNC NTKCVTIPST CSEIWGLSTP NTIDQWDTTG LYSFSEQTRS LDGRLQVSHR 120
  121 KGLPHVIYCR LWRWPDLHSH HELKAIENCE YAFNLKKDEV CVNPYHYQRV ETPV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	57.30103
Match:	1ozjA
Description:	Crystal structure of Smad3-MH1 bound to DNA at 2.4 A resolution
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [175-249]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LPPVLVPRHT EILTELPPLD DYTHSIPENT NFPAGIEPQS NYIPETPPPG YISEDGETSD  60
   61 QQLNQSMDTG SPAEL

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [250-467]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SPTTLSPVNH SLDLQPVTYS EPAFWCSIAY YELNQRVGET FHASQPSLTV DGFTDPSNSE  60
   61 RFCLGLLSNV NRNATVEMTR RHIGRGVRLY YIGGEVFAEC LSDSAIFVQS PNCNQRYGWH 120
  121 PATVCKIPPG CNLKIFNNQE FAALLAQSVN QGFEAVYQLT RMCTIRMSFV KGWGAEYRRQ 180
  181 TVTSTPCWIE LHLNGPLQWL DKVLTQMGSP SVRCSSMS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	106.0
Match:	1khxA
Description:	Smad2 MH2 domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
SMAD binding	9.3718253521769	bayes_pls_golite062009
R-SMAD binding	9.05113862383896	bayes_pls_golite062009
transforming growth factor beta receptor, cytoplasmic mediator activity	5.17758651944685	bayes_pls_golite062009
transmembrane receptor protein serine/threonine kinase signaling protein activity	4.95270065635384	bayes_pls_golite062009
co-SMAD binding	4.57538059815089	bayes_pls_golite062009
transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity	4.49077041445033	bayes_pls_golite062009
binding	3.6561903894619	bayes_pls_golite062009
transcription regulator activity	3.49687772656017	bayes_pls_golite062009
protein binding	3.44553762357492	bayes_pls_golite062009
molecular transducer activity	3.3543221973342	bayes_pls_golite062009
signal transducer activity	3.3543221973342	bayes_pls_golite062009
DNA binding	3.30334070294767	bayes_pls_golite062009
type I transforming growth factor beta receptor binding	3.25693690222359	bayes_pls_golite062009
nucleic acid binding	3.21526555447097	bayes_pls_golite062009
receptor signaling protein activity	3.08220855629618	bayes_pls_golite062009
transcription activator activity	2.94935902482394	bayes_pls_golite062009
receptor serine/threonine kinase binding	2.94401714632865	bayes_pls_golite062009
sequence-specific DNA binding	2.88406197124131	bayes_pls_golite062009
activin binding	2.85561990563659	bayes_pls_golite062009
transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity	2.75979335370845	bayes_pls_golite062009
RNA polymerase II transcription factor activity	2.61166537801555	bayes_pls_golite062009
transmembrane receptor protein serine/threonine kinase binding	2.57320437127906	bayes_pls_golite062009
transforming growth factor beta receptor binding	2.57320437127906	bayes_pls_golite062009
phosphatase activity	2.46582579847871	bayes_pls_golite062009
phosphoric ester hydrolase activity	2.41505949322677	bayes_pls_golite062009
promoter binding	2.30493918456602	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	2.1294440466744	bayes_pls_golite062009
transcription factor activity	2.08449567315174	bayes_pls_golite062009
collagen binding	1.9825610927799	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	1.88096476099716	bayes_pls_golite062009
kinase activity	1.82476774968305	bayes_pls_golite062009
transcription repressor activity	1.74929788315626	bayes_pls_golite062009
protein kinase activity	1.73373132141588	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	1.66058356077795	bayes_pls_golite062009
transforming growth factor beta receptor, common-partner cytoplasmic mediator activity	1.61493700485683	bayes_pls_golite062009
chromatin binding	1.44267609273288	bayes_pls_golite062009
structure-specific DNA binding	1.32552524966562	bayes_pls_golite062009
transferase activity	1.29860325699399	bayes_pls_golite062009
double-stranded DNA binding	1.21988722144674	bayes_pls_golite062009
protein serine/threonine kinase activity	1.1868962075754	bayes_pls_golite062009
receptor binding	1.1261895404991	bayes_pls_golite062009
histone binding	1.01074250987871	bayes_pls_golite062009
transcription factor binding	0.95553719139833	bayes_pls_golite062009
small conjugating protein ligase activity	0.9108432673413	bayes_pls_golite062009
ubiquitin-protein ligase activity	0.90981150861416	bayes_pls_golite062009
ubiquitin protein ligase binding	0.85140744915405	bayes_pls_golite062009
I-SMAD binding	0.605133087848961	bayes_pls_golite062009
RNA binding	0.403713641965787	bayes_pls_golite062009
cell adhesion molecule binding	0.372418193032456	bayes_pls_golite062009
enzyme binding	0.34998623523914	bayes_pls_golite062009
protein dimerization activity	0.33340925100096	bayes_pls_golite062009
specific transcriptional repressor activity	0.15013949452504	bayes_pls_golite062009
identical protein binding	0.0513801649373811	bayes_pls_golite062009
protein homodimerization activity	0.0339057097360133	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: