D-I-TASSER P12644-D2

D-I-TASSER results for P12644-D2

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

Input Sequence in FASTA format

>P12644 (166 residues)
VRSFHHEEHLENIPGTSENSAFRFLFNLSSIPENEVISSAELRLFREQVDQGPDWERGFH
RINIYEVMKPPAEVVPGHLITRLLDTRLVHHNVTRWETFDVSPAVLRWTREKQPNYGLAI
EVTHLHQTRTHQGQHVRISRSLPQGSGNWAQLRPLLVTFGHDGRGH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| VRSFHHEEHLENIPGTSENSAFRFLFNLSSIPENEVISSAELRLFREQVDQGPDWERGFHRINIYEVMKPPAEVVPGHLITRLLDTRLVHHNVTRWETFDVSPAVLRWTREKQPNYGLAIEVTHLHQTRTHQGQHVRISRSLPQGSGNWAQLRPLLVTFGHDGRGH
Prediction	CCCSSCCCCCCCCCCCCCCCSSSSSSSCCCCCCCCSSSSSSSSSSSSCCCCCCCCCCCCSSSSSSSSSCCCCCCCCCCCCSSSSSSSSSCCCCCSSSSSSHHHHHHHHHHCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCC
Confidence	9432013444566556887429999867889996537888889987047888766785189999999606755689886316888899527887179997699899999779888648999996799877730021112145678777523585899994588899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| VRSFHHEEHLENIPGTSENSAFRFLFNLSSIPENEVISSAELRLFREQVDQGPDWERGFHRINIYEVMKPPAEVVPGHLITRLLDTRLVHHNVTRWETFDVSPAVLRWTREKQPNYGLAIEVTHLHQTRTHQGQHVRISRSLPQGSGNWAQLRPLLVTFGHDGRGH
Prediction	7300425434644554576332202010351376340330102012433754454743312020020033444347454323302233044454223314035004303545553220111032445454455431415432444674454220000001234578
	Values range from 0 (buried residue) to 8 (highly exposed residue)

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

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of DeepPotential. 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.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCSSCCCCCCCCCCCCCCCSSSSSSSCCCCCCCCSSSSSSSSSSSSCCCCCCCCCCCCSSSSSSSSSCCCCCCCCCCCCSSSSSSSSSCCCCCSSSSSSHHHHHHHHHHCCCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCC
VRSFHHEEHLENIPGTSENSAFRFLFNLSSIPENEVISSAELRLFREQVDQGPDWERGFHRINIYEVMKPPAEVVPGHLITRLLDTRLVHHNVTRWETFDVSPAVLRWTREKQPNYGLAIEVTHLHQTRTHQGQHVRISRSLPQGSGNWAQLRPLLVTFGHDGRGH

4ycgA

0.25

0.22

6.93

1.17

DEthreader

VRSFSVE-DAI-STAATPFQKHILIFNI-SIPRHEQITRAELRLYVSCQNDVDSTHGLEGSMVVYDVLEDSETWDQATGTKTFLVSQDIR--DEGWETLEVSSAVKRWVRADTNKNKLEVTVQSHRE-SCDTL-DISVPPGS------K--NLPFFVVFSNDGKET

4ycgA

0.25

0.23

7.10

1.67

SPARKS-K

VRSFSVEDAISAATEDFPFQKHILIFNI-SIPRHEQITRAELRLYVSCQNDVDSTHGLEGSMVVYDVLEDSETWDQATGTKTFLVSQDIR--DEGWETLEVSSAVKRWVRADTNKNKLEVTVQSHRES----CDTLDISVPPGSKN------LPFFVVFSNDRSNG

4ycgA

0.24

0.22

6.94

1.16

MapAlign

VRSFSVEAISTAATEDFPFQKHILIFNI-SIPRHEQITRAELRLYVSCQNDVDSTHGLEGSMVVYDVLEDSETWDQATGTKTFLVSQDIRD--EGWETLEVSSAVKRWVDSTTNKNKLEVTVQSH----RESCDTLDISV------PPGSKNLPFFVVFSNDRSNG

4ycgA

0.24

0.22

6.95

1.11

CEthreader

VRSFSVEDAISTAATEDFPFQKHILIFNISIPRHEQITRAELRLYVSCQNDVDSTHGLEGSMVVYDVLEDSETWDQATGTKTFLVSQDIRD--EGWETLEVSSAVKRWVRADTNKNKLEVTVQSHR----ESCDTLDISVPPGS------KNLPFFVVFSNDRSNG

4ycgA

0.25

0.23

7.10

1.51

MUSTER

VRSFSVEDAISAATEDFPFQKHILIFNIS-IPRHEQITRAELRLYVSCQNDVDSTHGLEGSMVVYDVLEDSETWDQATGTKTFLVSQDIR--DEGWETLEVSSAVKRWVRADTNKNKLEVTVQSHRES----CDTLDISVPPGS------KNLPFFVVFSNDRSNG

4ycgA

0.25

0.23

7.10

3.50

HHsearch

VRSFSVEDAISAATEDFPFQKHILIFNIS-IPRHEQITRAELRLYVSCQNDVDSTHGLEGSMVVYDVLEDSETWDQATGTKTFLVSQDI--RDEGWETLEVSSAVKRWVRADSNKNKLEVTVQSHRES----CDTLDISV------PPGSKNLPFFVVFSNDRSNG

4ycgA

0.23

0.22

6.80

1.77

FFAS-3D

VRSFSVEDAISTAATEDFPFQKHILIFNISIPRHEQITRAELRLYVSCQNDVDSTHGLEGSMVVYDVLEDSETWDQATGTKTFLVSQDI--RDEGWETLEVSSAVKRWVRADSTTNKNKLEVTVQSHRESCDTLDI--------SVPPGSKNLPFFVVFSNDRSNG

4ycgA

0.21

0.19

6.10

1.05

EigenThreader

SNSFSVEDAIA--TEDFPFQKHILIFN-ISIPRHEQITRAELRLYVSCDVDSTHGLEGSMVVYDVLEDSET---WDQATGTKTFLVSQDIR-DEGWETLEVSSAVKRWVRADSTKNKLEVTVQSHRE---SCDTLDISVPPGSK-------NLPFFVVFDRSNGTK

4ycgA

0.25

0.23

7.10

2.10

CNFpred

VRSFSVEDAISTAATEDPFQKHILIFNIS-IPRHEQITRAELRLYVSCQNDVDSTHGLEGSMVVYDVLEDSETWDQATGTKTFLVSQDIR--DEGWETLEVSSAVKRWVRADSNKNKLEVTVQSHRES----CDTLDISVPP------GSKNLPFFVVFSNDRSNG

3rjrA

0.23

0.19

5.86

1.00

DEthreader

VTRVLMVESGIYFKGTP--HSLYMLFNTSEREVPEPLSRAELRLLRLKL-----K-VE-QHVELYQKYSQ--------DSWRYLSNRLLAPSDPEWLSFDVTGVVRQWLTRREAIEGFRLSAHCS-VE-IN--GDLATIHG-------MN--RPFLLLMATPLERA

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8458

(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 DeepPotential, 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	4ycgA	0.84	1.76	0.248	0.922	model1_4ycgA.pdb.gz
2	5hlyA2	0.67	2.83	0.157	0.807	model1_5hlyA2.pdb.gz
3	5ntuA	0.66	2.82	0.179	0.789	model1_5ntuA.pdb.gz
4	3rjrA	0.65	2.99	0.222	0.801	model1_3rjrA.pdb.gz
5	1pnfA	0.58	3.49	0.122	0.765	model1_1pnfA.pdb.gz
6	3ks7D1	0.58	3.18	0.047	0.771	model1_3ks7D1.pdb.gz
7	6ds5A	0.58	3.21	0.081	0.747	model1_6ds5A.pdb.gz
8	1gff1	0.58	3.84	0.036	0.819	model1_1gff1.pdb.gz
9	1kvpA	0.57	3.89	0.057	0.825	model1_1kvpA.pdb.gz
10	4r4xA	0.54	3.42	0.126	0.717	model1_4r4xA.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:0005102	0.96	receptor binding
GO:0005160	0.86	transforming growth factor beta receptor binding
GO:0005125	0.68	cytokine activity
GO:0033612	0.52	receptor serine/threonine kinase binding
GO:0070700	0.51	BMP receptor 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:0044699	0.99	single-organism process
GO:0065007	0.98	biological regulation
GO:0050794	0.97	regulation of cellular process
GO:0044767	0.97	single-organism developmental process
GO:0080090	0.96	regulation of primary metabolic process
GO:0060255	0.96	regulation of macromolecule metabolic process
GO:0031323	0.96	regulation of cellular metabolic process
GO:0009987	0.96	cellular process
GO:0048522	0.95	positive regulation of cellular process
GO:0044763	0.95	single-organism cellular process
GO:0007165	0.95	signal transduction
GO:0048583	0.93	regulation of response to stimulus
GO:0031325	0.93	positive regulation of cellular metabolic process
GO:0010604	0.93	positive regulation of macromolecule metabolic process
GO:0048856	0.89	anatomical structure development
GO:0010556	0.89	regulation of macromolecule biosynthetic process
GO:0048869	0.88	cellular developmental process
GO:0032268	0.86	regulation of cellular protein metabolic process
GO:0009967	0.86	positive regulation of signal transduction
GO:0001934	0.85	positive regulation of protein phosphorylation
GO:0042981	0.82	regulation of apoptotic process
GO:2000112	0.78	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.78	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.78	regulation of gene expression
GO:0007178	0.78	transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0043408	0.77	regulation of MAPK cascade
GO:0006355	0.77	regulation of transcription, DNA-templated
GO:0090100	0.76	positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0060395	0.75	SMAD protein signal transduction
GO:0010862	0.75	positive regulation of pathway-restricted SMAD protein phosphorylation
GO:0048519	0.69	negative regulation of biological process
GO:0048523	0.68	negative regulation of cellular process
GO:0006357	0.67	regulation of transcription from RNA polymerase II promoter
GO:0048468	0.66	cell development
GO:0031324	0.62	negative regulation of cellular metabolic process
GO:0030509	0.55	BMP signaling pathway
GO:0051239	0.54	regulation of multicellular organismal process
GO:2000026	0.53	regulation of multicellular organismal development
GO:0009653	0.53	anatomical structure morphogenesis
GO:0045595	0.51	regulation of cell differentiation
GO:0031327	0.50	negative regulation of cellular biosynthetic process
GO:0010605	0.50	negative regulation of macromolecule metabolic process

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:0044421	0.92	extracellular region part
GO:0005615	0.84	extracellular space
GO:0044464	0.74	cell part
GO:0044424	0.59	intracellular 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	0.066	1w0nA	0.488	3.12	0.067	0.626	3.2.1.55	NA
2	0.066	1gu3A	0.498	3.71	0.092	0.687	3.2.1.4	4
3	0.066	2j1eA	0.497	3.51	0.036	0.669	3.2.1.52	110
4	0.060	1piv1	0.563	4.00	0.087	0.813	3.4.22.29	NA
5	0.060	2nqaB	0.262	5.91	0.035	0.494	3.4.22.53 3.4.22.52	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.02	3iylB	0.536	4.39	0.090	0.855	0.39	MYR	complex1.pdb.gz	101,105,116,117,156,158
2	0.01	3mbw0	0.544	3.83	0.106	0.783	0.23	III	complex2.pdb.gz	28,106,107,108
3	0.01	1bhgA	0.549	3.47	0.097	0.741	0.11	UUU	complex3.pdb.gz	62,63,81
4	0.01	1vbe1	0.563	4.00	0.087	0.813	0.11	J78	complex4.pdb.gz	118,155,157,160
5	0.01	2qbxB	0.532	3.98	0.087	0.759	0.19	III	complex5.pdb.gz	25,26,27,30,116,117,118

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.