D-I-TASSER P37173-D1

D-I-TASSER results for P37173-D1

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

Input Sequence in FASTA format

>P37173 (153 residues)
MGRGLLRGLWPLHIVLWTRIASTIPPHVQKSVNNDMIVTDNNGAVKFPQLCKFCDVRFST
CDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPK
CIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGRGLLRGLWPLHIVLWTRIASTIPPHVQKSVNNDMIVTDNNGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY
Prediction	CCCCCCCCCCCSSSSSSSHHHHCCCCCCCCCCCCCSSSSCCCCCSSCCCCCCCSCCCCCCCCCCCSSSCCCCCSSSCCCCCSSSSSSSSSCCCCSSSSSSSCCCCCCCCCCSCCCCCCCCSSSSSCCCCCCCSSSSSCCCCCCCCSSSCCCCC
Confidence	972021243423444442122048985301146331553378853241113330575775589874734676144328964389999997399268999756999823671426899982588643689972799744843267457548899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGRGLLRGLWPLHIVLWTRIASTIPPHVQKSVNNDMIVTDNNGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY
Prediction	754330421230100011301432354236315441233366331414400410425354175553144413033216445300000035576413030203336342341305426364030454656713010000456504432314777
	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

CCCCCCCCCCCSSSSSSSHHHHCCCCCCCCCCCCCSSSSCCCCCSSCCCCCCCSCCCCCCCCCCCSSSCCCCCSSSCCCCCSSSSSSSSSCCCCSSSSSSSCCCCCCCCCCSCCCCCCCCSSSSSCCCCCCCSSSSSCCCCCCCCSSSCCCCC
MGRGLLRGLWPLHIVLWTRIASTIPPHVQKSVNNDMIVTDNNGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

1ploA

0.94

0.66

18.52

0.83

DEthreader

-----------------------------------------A--VKFPQLCKFCDVRFSTCDNQSCMS-NCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFS-N-

1ks6A

0.60

0.42

11.99

3.08

SPARKS-K

---------------------------------------------QLPRLCKFCDVKATTCSNQDQCTSNCNITSICEKNNEVCAAVWRRNDENVTLETICHDPQKRLYGHMLDDSSSEQCVMKEKKDDGGLMFMCSCTGEECNDVLIFSAI-

1ks6A

0.62

0.42

11.97

1.13

MapAlign

----------------------------------------------LPRLCKFCDVKATTCSNQDQCTSNCNITSICEKNNEVCAAVWRRNDENVTLETICHDPQKRLYGHMLDDSSSEQCVMKEKKDDGGLMFMCSCTGEECNDVLIFS---

1ks6A

0.60

0.42

11.99

1.18

CEthreader

---------------------------------------------QLPRLCKFCDVKATTCSNQDQCTSNCNITSICEKNNEVCAAVWRRNDENVTLETICHDPQKRLYGHMLDDSSSEQCVMKEKKDDGGLMFMCSCTGEECNDVLIFSAI-

1ploA

0.99

0.75

21.05

2.14

MUSTER

-------------------------------------VTDNAGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

1ploA

0.99

0.75

21.05

4.94

HHsearch

-------------------------------------VTDNAGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

1ploA

0.99

0.75

20.87

1.47

FFAS-3D

--------------------------------------TDNAGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

1ploA

0.96

0.71

19.97

0.97

EigenThreader

-------------------------------------VTDNAGAVKFPQLCKFC---DVRCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

1ktzB

1.00

0.69

19.40

3.06

CNFpred

-----------------------------------------------PQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

1ks6A

0.58

0.40

11.46

0.83

DEthreader

--------------------------------------------Q-LPRLCKFCDVKATTCSNQQCTSN-CNITSICEKNNEVCAAVWRRNDENVTLETICHDPQKRLYGHMLDDSSSEQCVMKEKKDDGGLMFMCSCTGEECNDVLIFS-AI

(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	0.6436

(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	1ploA	0.66	2.26	0.974	0.752	model1_1ploA.pdb.gz
2	1ks6A	0.65	1.47	0.589	0.699	model1_1ks6A.pdb.gz
3	6gbiA	0.46	2.71	0.116	0.562	model1_6gbiA.pdb.gz
4	6eqoA	0.44	5.15	0.065	0.804	model1_6eqoA.pdb.gz
5	5w1uA	0.44	5.57	0.101	0.863	model1_5w1uA.pdb.gz
6	6e7kC	0.44	1.95	0.215	0.497	model1_6e7kC.pdb.gz
7	4be4A	0.44	5.41	0.058	0.830	model1_4be4A.pdb.gz
8	6iomA	0.44	3.65	0.105	0.608	model1_6iomA.pdb.gz
9	1hq0A	0.44	4.69	0.031	0.719	model1_1hq0A.pdb.gz
10	1qo0B1	0.43	4.79	0.033	0.758	model1_1qo0B1.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	0.84	receptor binding
GO:0005160	0.83	transforming growth factor beta receptor binding
GO:0050431	0.82	transforming growth factor beta binding
GO:0034713	0.82	type I transforming growth factor beta receptor binding
GO:0003824	0.60	catalytic activity
GO:0016740	0.57	transferase activity
GO:0004871	0.57	signal transducer activity
GO:0038023	0.56	signaling receptor activity
GO:0016301	0.56	kinase activity
GO:0019199	0.55	transmembrane receptor protein kinase activity
GO:0004674	0.55	protein serine/threonine kinase activity
GO:0005024	0.54	transforming growth factor beta-activated receptor activity

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:0044763	1.00	single-organism cellular process
GO:0065007	0.98	biological regulation
GO:0050794	0.97	regulation of cellular process
GO:2000026	0.96	regulation of multicellular organismal development
GO:0051094	0.96	positive regulation of developmental process
GO:0048522	0.96	positive regulation of cellular process
GO:0048513	0.96	animal organ development
GO:0044767	0.96	single-organism developmental process
GO:0030154	0.96	cell differentiation
GO:0009653	0.96	anatomical structure morphogenesis
GO:0051240	0.83	positive regulation of multicellular organismal process
GO:0051128	0.83	regulation of cellular component organization
GO:0045597	0.83	positive regulation of cell differentiation
GO:0022603	0.83	regulation of anatomical structure morphogenesis
GO:0010718	0.82	positive regulation of epithelial to mesenchymal transition
GO:0007507	0.82	heart development
GO:0001775	0.82	cell activation
GO:0030324	0.80	lung development
GO:0051272	0.67	positive regulation of cellular component movement
GO:0040017	0.67	positive regulation of locomotion
GO:0030335	0.66	positive regulation of cell migration
GO:0008152	0.58	metabolic process
GO:0071704	0.56	organic substance metabolic process
GO:0050896	0.55	response to stimulus
GO:0044238	0.55	primary metabolic process
GO:0044237	0.55	cellular metabolic process
GO:0043170	0.55	macromolecule metabolic process
GO:0016043	0.55	cellular component organization
GO:0007165	0.55	signal transduction
GO:0044260	0.54	cellular macromolecule metabolic process
GO:0060317	0.53	cardiac epithelial to mesenchymal transition
GO:0048762	0.53	mesenchymal cell differentiation
GO:0001654	0.53	eye development
GO:0044267	0.52	cellular protein metabolic process
GO:0010033	0.52	response to organic substance
GO:0007167	0.52	enzyme linked receptor protein signaling pathway
GO:1901700	0.51	response to oxygen-containing compound
GO:0014070	0.51	response to organic cyclic compound
GO:0007179	0.51	transforming growth factor beta receptor signaling pathway
GO:0006464	0.51	cellular protein modification process
GO:0033993	0.50	response to lipid
GO:0006468	0.50	protein phosphorylation

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:0016020	1.00	membrane
GO:0044464	0.87	cell part
GO:0044424	0.67	intracellular part
GO:0044425	0.62	membrane part
GO:0045121	0.59	membrane raft
GO:0032991	0.53	macromolecular complex
GO:0043234	0.51	protein complex
GO:0005886	0.50	plasma membrane

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	0.549	1ploA	0.659	2.26	0.974	0.752	2.7.11.30	51,59,61,67,69,88,98,113,115,118,121,123,126,134,143,145,147,149
2	0.060	1keuA	0.389	5.60	0.071	0.758	4.2.1.46	NA
3	0.060	2vr5A	0.407	5.33	0.032	0.745	3.2.1.-	NA
4	0.060	2jenA	0.412	5.18	0.081	0.758	3.2.1.4	116
5	0.060	2h62D	0.399	3.11	0.056	0.529	2.7.11.30	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:

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
	1	0.02	1nys2	0.424	2.93	0.169	0.536	0.48	III	complex1.pdb.gz	85,87,89,132

	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.