D-I-TASSER P42224

D-I-TASSER results for P42224

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: P42224
Protein Name: Signal transducer and activator of transcription 1-alpha/beta
Gene Name: STAT1

Input Sequence in FASTA format

>P42224 (750 residues)
MSQWYELQQLDSKFLEQVHQLYDDSFPMEIRQYLAQWLEKQDWEHAANDVSFATIRFHDL
LSQLDDQYSRFSLENNFLLQHNIRKSKRNLQDNFQEDPIQMSMIIYSCLKEERKILENAQ
RFNQAQSGNIQSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNR
EHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWK
RRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQV
LWDRTFSLFQQLIQSSFVVERQPCMPTHPQRPLVLKTGVQFTVKLRLLVKLQELNYNLKV
KVLFDKDVNERNTVKGFRKFNILGTHTKVMNMEESTNGSLAAEFRHLQLKEQKNAGTRTN
EGPLIVTEELHSLSFETQLCQPGLVIDLETTSLPVVVISNVSQLPSGWASILWYNMLVAE
PRNLSFFLTPPCARWAQLSEVLSWQFSSVTKRGLNVDQLNMLGEKLLGPNASPDGLIPWT
RFCKENINDKNFPFWLWIESILELIKKHLLPLWNDGCIMGFISKERERALLKDQQPGTFL
LRFSESSREGAITFTWVERSQNGGEPDFHAVEPYTKKELSAVTFPDIIRNYKVMAAENIP
ENPLKYLYPNIDKDHAFGKYYSRPKEAPEPMELDGPKGTGYIKTELISVSEVHPSRLQTT
DNLLPMSPEEFDEVSRIVGSVEFDSMMNTV

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	P42224-D1	1-128	128		MSQWYELQQLDSKFLEQVHQLYDDSFPMEIRQYLAQWLEKQDWEHAANDVSFATIRFHDLLSQLDDQYSRFSLENNFLLQHNIRKSKRNLQDNFQEDPIQMSMIIYSCLKEERKILENAQRFNQAQSG
2	P42224-D2	129-317	189		NIQSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRTFSLFQQLIQSSF
3	P42224-D3	318-458	141		VVERQPCMPTHPQRPLVLKTGVQFTVKLRLLVKLQELNYNLKVKVLFDKDVNERNTVKGFRKFNILGTHTKVMNMEESTNGSLAAEFRHLQLKEQKNAGTRTNEGPLIVTEELHSLSFETQLCQPGLVIDLETTSLPVVVI
4	P42224-D4	459-750	292		SNVSQLPSGWASILWYNMLVAEPRNLSFFLTPPCARWAQLSEVLSWQFSSVTKRGLNVDQLNMLGEKLLGPNASPDGLIPWTRFCKENINDKNFPFWLWIESILELIKKHLLPLWNDGCIMGFISKERERALLKDQQPGTFLLRFSESSREGAITFTWVERSQNGGEPDFHAVEPYTKKELSAVTFPDIIRNYKVMAAENIPENPLKYLYPNIDKDHAFGKYYSRPKEAPEPMELDGPKGTGYIKTELISVSEVHPSRLQTTDNLLPMSPEEFDEVSRIVGSVEFDSMMNTV

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.81

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1yvlB	0.86	1.13	0.975	0.871	model1_1yvlB.pdb.gz
2	1bg1A	0.72	1.73	0.546	0.737	model1_1bg1A.pdb.gz
3	6ux2A	0.68	2.05	0.377	0.707	model1_6ux2A.pdb.gz
4	1y1uA	0.62	3.16	0.309	0.681	model1_1y1uA.pdb.gz
5	4y5uA	0.54	2.66	0.304	0.576	model1_4y5uA.pdb.gz
6	1uusA	0.46	5.07	0.152	0.564	model1_1uusA.pdb.gz
7	4h7uA	0.16	8.02	0.040	0.256	model1_4h7uA.pdb.gz
8	3hhmB	0.16	4.06	0.039	0.179	model1_3hhmB.pdb.gz
9	2ptkA1	0.14	4.04	0.113	0.161	model1_2ptkA1.pdb.gz
10	2blmA	0.14	5.06	0.069	0.168	model1_2blmA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003700	0.68	transcription factor activity, sequence-specific DNA binding
GO:1901363	0.59	heterocyclic compound binding
GO:0097159	0.59	organic cyclic compound binding
GO:0003676	0.53	nucleic acid binding
GO:0003677	0.51	DNA binding
GO:0000981	0.50	RNA polymerase II transcription factor activity, sequence-specific DNA binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0065007	0.96	biological regulation
GO:0050789	0.95	regulation of biological process
GO:0050794	0.94	regulation of cellular process
GO:0009987	0.93	cellular process
GO:0048518	0.88	positive regulation of biological process
GO:0044699	0.82	single-organism process
GO:0007165	0.82	signal transduction
GO:0080090	0.79	regulation of primary metabolic process
GO:0060255	0.79	regulation of macromolecule metabolic process
GO:0048522	0.79	positive regulation of cellular process
GO:0031323	0.79	regulation of cellular metabolic process
GO:0009889	0.76	regulation of biosynthetic process
GO:0050896	0.75	response to stimulus
GO:0006355	0.75	regulation of transcription, DNA-templated
GO:0007259	0.74	JAK-STAT cascade
GO:0044763	0.72	single-organism cellular process
GO:0010033	0.70	response to organic substance
GO:0070887	0.68	cellular response to chemical stimulus
GO:0071310	0.67	cellular response to organic substance
GO:0048869	0.66	cellular developmental process
GO:0031325	0.64	positive regulation of cellular metabolic process
GO:0010604	0.64	positive regulation of macromolecule metabolic process
GO:0051239	0.63	regulation of multicellular organismal process
GO:0050793	0.63	regulation of developmental process
GO:0045935	0.63	positive regulation of nucleobase-containing compound metabolic process
GO:0042127	0.63	regulation of cell proliferation
GO:0031328	0.63	positive regulation of cellular biosynthetic process
GO:0010628	0.63	positive regulation of gene expression
GO:0010557	0.63	positive regulation of macromolecule biosynthetic process
GO:0045893	0.62	positive regulation of transcription, DNA-templated
GO:0032501	0.62	multicellular organismal process
GO:0007166	0.61	cell surface receptor signaling pathway
GO:0034097	0.60	response to cytokine
GO:0019221	0.60	cytokine-mediated signaling pathway
GO:0008284	0.60	positive regulation of cell proliferation
GO:0030154	0.59	cell differentiation
GO:2000026	0.57	regulation of multicellular organismal development
GO:0045595	0.57	regulation of cell differentiation
GO:0048583	0.56	regulation of response to stimulus
GO:0009719	0.56	response to endogenous stimulus
GO:1901700	0.55	response to oxygen-containing compound
GO:0048519	0.55	negative regulation of biological process
GO:0009725	0.54	response to hormone
GO:0048523	0.52	negative regulation of cellular process
GO:0014070	0.52	response to organic cyclic compound
GO:0051246	0.50	regulation of protein metabolic process
GO:0009605	0.50	response to external stimulus

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	1.00	intracellular part
GO:0043226	0.94	organelle
GO:0005737	0.94	cytoplasm
GO:0043229	0.93	intracellular organelle
GO:0043227	0.92	membrane-bounded organelle
GO:0005634	0.91	nucleus
GO:0044446	0.63	intracellular organelle part
GO:0044428	0.58	nuclear part

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	1ofdA	0.311	8.50	0.040	0.505	1.4.7.1	NA
2	0.060	2dqmA	0.293	8.33	0.041	0.467	3.4.11.2	NA
3	0.060	1fo4A	0.310	8.01	0.034	0.479	1.17.1.4	NA
4	0.060	1clqA	0.309	8.53	0.031	0.500	2.7.7.7	NA
5	0.060	3iayA	0.286	8.55	0.041	0.467	2.7.7.7	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.