D-I-TASSER P37023-D1

D-I-TASSER results for P37023-D1

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

Input Sequence in FASTA format

>P37023 (154 residues)
MTLGSPRKGLLMLLMALVTQGDPVKPSRGPLVTCTCESPHCKGPTCRGAWCTVVLVREEG
RHPQEHRGCGNLHRELCRGRPTEFVNHYCCDSHLCNHNVSLVLEATQPPSEQPGTDGQLA
LILGPVLALLALVALGVLGLWHVRRRQEKQRGLH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTLGSPRKGLLMLLMALVTQGDPVKPSRGPLVTCTCESPHCKGPTCRGAWCTVVLVREEGRHPQEHRGCGNLHRELCRGRPTEFVNHYCCDSHLCNHNVSLVLEATQPPSEQPGTDGQLALILGPVLALLALVALGVLGLWHVRRRQEKQRGLH
Prediction	CCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCSSSSSCCCCCCCCCSSCSSSSSSSSSCCCCSSSSSSCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence	9865420125554333268876655567861799817999999834204899999982898399983777651110378998872677379744489996556788888888875522136899999999999999997888887677774479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTLGSPRKGLLMLLMALVTQGDPVKPSRGPLVTCTCESPHCKGPTCRGAWCTVVLVREEGRHPQEHRGCGNLHRELCRGRPTEFVNHYCCDSHLCNHNVSLVLEATQPPSEQPGTDGQLALILGPVLALLALVALGVLGLWHVRRRQEKQRGLH
Prediction	7535334310000001122573745646543240303367176530412201112335775433434212542543144443752324003341115614351444644575563432000112133101213212010011034345545748
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCSSSSSCCCCCCCCCSSCSSSSSSSSSCCCCSSSSSSCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
MTLGSPRKGLLMLLMALVTQGDPVKPSRGPLVTCTCESPHCKGPTCRGAWCTVVLVREEGRHPQEHRGCGNLHRELCRGRPTEFVNHYCCDSHLCNHNVSLVLEATQPPSEQPGTDGQLALILGPVLALLALVALGVLGLWHVRRRQEKQRGLH

4faoC

1.00

0.49

13.64

1.97

SPARKS-K

-----------------------------PLVTCTCESPHCKGPTCRGAWCTVVLVREEGRHPQEHRGCGNLHRELCRGRPTEFVNHYCCDSHLCNHNVSLVLE--------------------------------------------------

4faoC

1.00

0.49

13.64

1.41

MUSTER

-----------------------------PLVTCTCESPHCKGPTCRGAWCTVVLVREEGRHPQEHRGCGNLHRELCRGRPTEFVNHYCCDSHLCNHNVSLVLE--------------------------------------------------

4faoC

1.00

0.49

13.64

2.28

HHsearch

-----------------------------PLVTCTCESPHCKGPTCRGAWCTVVLVREEGRHPQEHRGCGNLHRELCRGRPTEFVNHYCCDSHLCNHNVSLVLE--------------------------------------------------

4faoC

1.00

0.49

13.64

1.15

CNFpred

-----------------------------PLVTCTCESPHCKGPTCRGAWCTVVLVREEGRHPQEHRGCGNLHRELCRGRPTEFVNHYCCDSHLCNHNVSLVLE--------------------------------------------------

4l79A

0.11

0.08

3.06

0.83

DEthreader

ELHIDYFNNAIICDLIENGILAMLDEELRGTFELNSRTTLP--H-S----CFRIQHYA----GKVLYQVEFVNAGSFK--RYLG-------------------E--RAGARNPRTLFQLEDLRKQRLEDLATLIQKIYRGWKCRTHFLLMKGLN

2qjbD

0.22

0.12

3.69

1.68

SPARKS-K

---------------------------TLPFLKCYCSPEDAINNTCINGHCFTMIEEDDQGETTLTSGCLGLEGSQCRDTPIQRRSIECCRTNLCNQYLQPTLPPVVIG---------------------------------------------

6iomA

0.13

0.09

3.14

0.71

MapAlign

HGLLAFIQLQQCAQDRCNAKLNLTSAYPPNGVECYSCVQGTSPPVVSCKGCFDGNVTLNVTVSLPVRGCVQDEFCTRDGVTGFTLSGSCCQGSRCNSDLRNKTYF-------------------------------------------------

2qjbD

0.20

0.10

3.34

0.72

CEthreader

---------------------------TLPFLKCYCSHHCPENTCITNGHCFTMIEEDDQGETTLTSGCLGLSDFQCRDTPHQRRSIECCRTNLCNQYLQPTLPPVVIG---------------------------------------------

2qjbD

0.22

0.12

3.69

1.18

MUSTER

---------------------------TLPFLKCYCSHHDAINNTCINGHCFTMIEEDDQGETTLTSGCLGLEGFQCRDTPIQRRSIECCRTNLCNQYLQPTLPPVVIG---------------------------------------------

2qjbD

0.23

0.12

3.86

2.05

HHsearch

---------------------------TLPFLKCYCSHH-CPNNTCINGHCFTMIEEDDQGETTLTSGCLGLEDFQCRDTPIQRRSIECCRTNLCNQYLQPTLPPVVIG---------------------------------------------

(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	0.5202

(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	3hd6A	0.47	5.30	0.068	0.818	model1_3hd6A.pdb.gz
2	2b2jA	0.47	4.85	0.043	0.760	model1_2b2jA.pdb.gz
3	6eu6A	0.47	4.95	0.054	0.760	model1_6eu6A.pdb.gz
4	4av3A	0.47	4.87	0.064	0.786	model1_4av3A.pdb.gz
5	5aezA	0.47	5.35	0.080	0.812	model1_5aezA.pdb.gz
6	4a01A	0.47	4.73	0.043	0.773	model1_4a01A.pdb.gz
7	3ikmD1	0.46	4.97	0.039	0.779	model1_3ikmD1.pdb.gz
8	7cq5C1	0.46	4.63	0.054	0.740	model1_7cq5C1.pdb.gz
9	6h7wB	0.46	4.31	0.083	0.695	model1_6h7wB.pdb.gz
10	3o0rB	0.46	5.00	0.019	0.727	model1_3o0rB.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:0098821	1.00	BMP receptor activity
GO:0050431	0.72	transforming growth factor beta binding
GO:0046332	0.72	SMAD binding
GO:0005025	0.72	transforming growth factor beta receptor activity, type I
GO:1901363	0.57	heterocyclic compound binding
GO:0097159	0.57	organic cyclic compound binding
GO:0097367	0.54	carbohydrate derivative binding
GO:0036094	0.54	small molecule binding
GO:0044877	0.53	macromolecular complex binding
GO:0035639	0.53	purine ribonucleoside triphosphate binding
GO:0032555	0.53	purine ribonucleotide binding
GO:0032550	0.53	purine ribonucleoside binding
GO:0032403	0.52	protein complex binding
GO:0019899	0.52	enzyme binding
GO:0005524	0.52	ATP binding
GO:0048185	0.51	activin binding
GO:0019901	0.51	protein kinase binding
GO:0016361	0.50	activin receptor activity, type I

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:0050896	1.00	response to stimulus
GO:0009987	1.00	cellular process
GO:0065007	0.88	biological regulation
GO:0050789	0.87	regulation of biological process
GO:0050794	0.85	regulation of cellular process
GO:0071704	0.81	organic substance metabolic process
GO:0044238	0.81	primary metabolic process
GO:0044237	0.81	cellular metabolic process
GO:0044260	0.80	cellular macromolecule metabolic process
GO:0007165	0.80	signal transduction
GO:0016043	0.79	cellular component organization
GO:0007166	0.79	cell surface receptor signaling pathway
GO:0006464	0.79	cellular protein modification process
GO:0007179	0.78	transforming growth factor beta receptor signaling pathway
GO:0006468	0.78	protein phosphorylation
GO:0071495	0.77	cellular response to endogenous stimulus
GO:0071363	0.77	cellular response to growth factor stimulus
GO:0071560	0.76	cellular response to transforming growth factor beta stimulus
GO:0044699	0.69	single-organism process
GO:0048518	0.62	positive regulation of biological process
GO:0044763	0.61	single-organism cellular process
GO:0032502	0.61	developmental process
GO:0019222	0.61	regulation of metabolic process
GO:0080090	0.60	regulation of primary metabolic process
GO:0060255	0.60	regulation of macromolecule metabolic process
GO:0048522	0.60	positive regulation of cellular process
GO:0044767	0.60	single-organism developmental process
GO:0031323	0.60	regulation of cellular metabolic process
GO:0048519	0.59	negative regulation of biological process
GO:0031325	0.59	positive regulation of cellular metabolic process
GO:0010604	0.59	positive regulation of macromolecule metabolic process
GO:0048856	0.58	anatomical structure development
GO:0048523	0.58	negative regulation of cellular process
GO:0031326	0.58	regulation of cellular biosynthetic process
GO:0051246	0.57	regulation of protein metabolic process
GO:0051239	0.57	regulation of multicellular organismal process
GO:0048583	0.57	regulation of response to stimulus
GO:0045893	0.57	positive regulation of transcription, DNA-templated
GO:0032501	0.57	multicellular organismal process
GO:0019220	0.57	regulation of phosphate metabolic process
GO:0009653	0.57	anatomical structure morphogenesis
GO:2000026	0.56	regulation of multicellular organismal development
GO:0065008	0.56	regulation of biological quality
GO:0051240	0.56	positive regulation of multicellular organismal process
GO:0048869	0.56	cellular developmental process
GO:0048584	0.56	positive regulation of response to stimulus
GO:0044707	0.56	single-multicellular organism process
GO:0009966	0.56	regulation of signal transduction
GO:0008285	0.56	negative regulation of cell proliferation
GO:0001936	0.56	regulation of endothelial cell proliferation
GO:0001934	0.56	positive regulation of protein phosphorylation
GO:0090100	0.55	positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0072132	0.55	mesenchyme morphogenesis
GO:0071773	0.55	cellular response to BMP stimulus
GO:0060841	0.55	venous blood vessel development
GO:0060562	0.55	epithelial tube morphogenesis
GO:0051241	0.55	negative regulation of multicellular organismal process
GO:0051128	0.55	regulation of cellular component organization
GO:0051094	0.55	positive regulation of developmental process
GO:0048844	0.55	artery morphogenesis
GO:0045944	0.55	positive regulation of transcription from RNA polymerase II promoter
GO:0045934	0.55	negative regulation of nucleobase-containing compound metabolic process
GO:0045597	0.55	positive regulation of cell differentiation
GO:0044087	0.55	regulation of cellular component biogenesis
GO:0040008	0.55	regulation of growth
GO:0032989	0.55	cellular component morphogenesis
GO:0032879	0.55	regulation of localization
GO:0031327	0.55	negative regulation of cellular biosynthetic process
GO:0030855	0.55	epithelial cell differentiation
GO:0030510	0.55	regulation of BMP signaling pathway
GO:0030155	0.55	regulation of cell adhesion
GO:0016477	0.55	cell migration
GO:0010629	0.55	negative regulation of gene expression
GO:0003013	0.55	circulatory system process
GO:0001525	0.55	angiogenesis
GO:2000279	0.54	negative regulation of DNA biosynthetic process
GO:0090500	0.54	endocardial cushion to mesenchymal transition
GO:0061298	0.54	retina vasculature development in camera-type eye
GO:0061154	0.54	endothelial tube morphogenesis
GO:0060840	0.54	artery development
GO:0060836	0.54	lymphatic endothelial cell differentiation
GO:0051895	0.54	negative regulation of focal adhesion assembly
GO:0043537	0.54	negative regulation of blood vessel endothelial cell migration
GO:0035912	0.54	dorsal aorta morphogenesis
GO:0035313	0.54	wound healing, spreading of epidermal cells
GO:0030513	0.54	positive regulation of BMP signaling pathway
GO:0030509	0.54	BMP signaling pathway
GO:0030308	0.54	negative regulation of cell growth
GO:0010862	0.54	positive regulation of pathway-restricted SMAD protein phosphorylation
GO:0008217	0.54	regulation of blood pressure
GO:0008015	0.54	blood circulation
GO:0003203	0.54	endocardial cushion morphogenesis
GO:0001974	0.54	blood vessel remodeling
GO:0001946	0.54	lymphangiogenesis

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:0005886	1.00	plasma membrane
GO:0044425	0.55	membrane part
GO:0044459	0.52	plasma membrane part
GO:0016021	0.52	integral component of membrane
GO:0005887	0.51	integral component of plasma membrane
GO:0009986	0.50	cell surface

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	1rqiA	0.418	4.41	0.048	0.643	2.5.1.10	NA
2	0.060	1xmeA	0.420	4.58	0.040	0.656	1.9.3.1	NA
3	0.060	2nztA	0.379	4.94	0.024	0.610	2.7.1.1	NA
4	0.060	3fieA	0.430	4.68	0.048	0.695	3.4.24.69	NA
5	0.060	1qs0A	0.419	5.35	0.037	0.747	1.2.4.4	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	0.05	2h622	0.430	1.96	0.211	0.493	0.99	III	complex1.pdb.gz	40,41,48,52,69,71,73,75,76,79,85,87
2	0.03	2goo0	0.438	2.00	0.208	0.500	0.72	III	complex2.pdb.gz	33,35,43,44,45,94,97
3	0.01	1qhaB	0.442	4.81	0.020	0.688	0.51	MG	complex3.pdb.gz	32,70,71
4	0.01	1hkbA	0.406	5.01	0.061	0.688	0.52	CA	complex4.pdb.gz	36,37,68,70

	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.