D-I-TASSER P36896-D2

D-I-TASSER results for P36896-D2

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

Input Sequence in FASTA format

>P36896 (174 residues)
GHLKEPEHPSMWGPVELVGIIAGPVFLLFLIIIIVFLVINYHQRVYHNRQRLDMEDPSCE
MCLSKDKTLQDLVYDLSTSGSGSGLPLFVQRTVARTIVLQEIIGKGRFGEVWRGRWRGGD
VAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GHLKEPEHPSMWGPVELVGIIAGPVFLLFLIIIIVFLVINYHQRVYHNRQRLDMEDPSCEMCLSKDKTLQDLVYDLSTSGSGSGLPLFVQRTVARTIVLQEIIGKGRFGEVWRGRWRGGDVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDY
Prediction	CCCCCCCCCCCCCHHHHSSSHHHHHHHHHHHHHHHHHHHHHHSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCHHHHCSSSSSSSCCCCSSSSSSSSCCCSSSSSSSCCCCHHHHHHHHHHHHHHCCCCCCSCSSSSSSSCCCCCCCSSSSSSSC
Confidence	998999899988803402102799999999887554323210000123455343444333457898742112345567999888762122210320604457751577079999998937899996563067899999999974589843434889997289997369999849
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GHLKEPEHPSMWGPVELVGIIAGPVFLLFLIIIIVFLVINYHQRVYHNRQRLDMEDPSCEMCLSKDKTLQDLVYDLSTSGSGSGLPLFVQRTVARTIVLQEIIGKGRFGEVWRGRWRGGDVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDY
Prediction	864754754654420200000211220304440400200222223446455464655435453465542443345444444434243434422264050342015222030120405744000221447745413302103414514041001000002346743220000028
	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

CCCCCCCCCCCCCHHHHSSSHHHHHHHHHHHHHHHHHHHHHHSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCHHHHCSSSSSSSCCCCSSSSSSSSCCCSSSSSSSCCCCHHHHHHHHHHHHHHCCCCCCSCSSSSSSSCCCCCCCSSSSSSSC
GHLKEPEHPSMWGPVELVGIIAGPVFLLFLIIIIVFLVINYHQRVYHNRQRLDMEDPSCEMCLSKDKTLQDLVYDLSTSGSGSGLPLFVQRTVARTIVLQEIIGKGRFGEVWRGRWRGGDVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDY

3kcfC1

0.88

0.56

15.85

1.99

SPARKS-K

--------------------------------------------------------------ISEGTTLKDLIYDMTTSGSGSGLPLLVQRTIARTIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDY

3kcfC1

0.88

0.56

15.85

1.58

MUSTER

--------------------------------------------------------------ISEGTTLKDLIYDMTTSGSGSGLPLLVQRTIARTIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDY

3kcfC1

0.88

0.56

15.85

1.59

FFAS-3D

--------------------------------------------------------------ISEGTTLKDLIYDMTTSGSGSGLPLLVQRTIARTIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDY

1b6cB

0.91

0.56

15.67

1.27

CNFpred

-------------------------------------------------------------------TLKDLIYDMTTSGSGSGLPLLVQRTIARTIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDY

1k9aB

0.18

0.11

3.73

0.83

DEthreader

-------------------------------------DADGLCTR--LIK-PKVMEGTV-AA---------Q-DEFYR-SGW--A----L-N-MKELKLLQTIGKGEFGDVMLGDYRGNKVAVKCIKDATAQAFLAEASVMTQL-RHSN-LVQLLGVIVEEK---GGLYIVTEY

3h9rA1

0.66

0.42

11.97

1.81

SPARKS-K

------------------------------------------------------------TTNVGDSTLADLLDHSCTSGSGSGLPFLVQRTVARQITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSST---QLWLITHY

3mdyA1

0.65

0.40

11.48

0.45

MapAlign

------------------------------------------------------------------ESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDY

3mdyA

0.65

0.40

11.48

0.31

CEthreader

------------------------------------------------------------------ESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDY

3h9rA1

0.66

0.42

11.97

1.54

MUSTER

------------------------------------------------------------TTNVGDSTLADLLDHSCTSGSGSGLPFLVQRTVARQITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSST---QLWLITHY

4oliA

0.19

0.18

5.74

0.77

HHsearch

SDPGVGLGALSRERIPWLGLSTMWGFGATLLEICFD-----GEAPLQSRSPSHFYQRQHRLPEPSCPQLATLTSQCLTYEPTQRPSFRDLTFHKRYLKKIRDLGEGHFGKVSLYCYDGEMVAVKALHR---SGWKQEIDILRT--LYHEHIIKYKGCCEDQGE--KSLQLVMEY

(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	0.5223

(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	3kcfC	0.59	1.58	0.820	0.638	model1_3kcfC.pdb.gz
2	3h9rA1	0.57	1.86	0.645	0.626	model1_3h9rA1.pdb.gz
3	3mdyA1	0.57	1.58	0.648	0.621	model1_3mdyA1.pdb.gz
4	1k9aB	0.49	3.58	0.211	0.615	model1_1k9aB.pdb.gz
5	6x88A	0.47	4.68	0.062	0.701	model1_6x88A.pdb.gz
6	6ka4A	0.47	4.95	0.063	0.799	model1_6ka4A.pdb.gz
7	7askF	0.47	5.45	0.091	0.805	model1_7askF.pdb.gz
8	3c4wB	0.47	4.14	0.121	0.615	model1_3c4wB.pdb.gz
9	6q2fA	0.47	4.03	0.017	0.661	model1_6q2fA.pdb.gz
10	2fo0A	0.47	3.60	0.127	0.603	model1_2fo0A.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:0016740	0.94	transferase activity
GO:0004672	0.93	protein kinase activity
GO:0004674	0.84	protein serine/threonine kinase activity
GO:0004871	0.82	signal transducer activity
GO:0004888	0.78	transmembrane signaling receptor activity
GO:0004675	0.77	transmembrane receptor protein serine/threonine kinase activity
GO:0005024	0.66	transforming growth factor beta-activated receptor activity
GO:0019838	0.63	growth factor binding
GO:0005025	0.63	transforming growth factor beta receptor activity, type I
GO:0050431	0.59	transforming growth factor beta binding
GO:0005057	0.58	receptor signaling protein 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:0065007	0.97	biological regulation
GO:0050789	0.97	regulation of biological process
GO:0044699	0.95	single-organism process
GO:0009987	0.95	cellular process
GO:0050794	0.93	regulation of cellular process
GO:0032502	0.91	developmental process
GO:0044767	0.88	single-organism developmental process
GO:0048518	0.86	positive regulation of biological process
GO:0044763	0.83	single-organism cellular process
GO:0048856	0.82	anatomical structure development
GO:0051239	0.81	regulation of multicellular organismal process
GO:0009653	0.79	anatomical structure morphogenesis
GO:0050793	0.78	regulation of developmental process
GO:0048869	0.78	cellular developmental process
GO:2000026	0.77	regulation of multicellular organismal development
GO:0042127	0.66	regulation of cell proliferation
GO:0031323	0.62	regulation of cellular metabolic process
GO:0080090	0.61	regulation of primary metabolic process
GO:0071704	0.61	organic substance metabolic process
GO:0060255	0.61	regulation of macromolecule metabolic process
GO:0007165	0.61	signal transduction
GO:0044260	0.60	cellular macromolecule metabolic process
GO:0048522	0.59	positive regulation of cellular process
GO:0007166	0.58	cell surface receptor signaling pathway
GO:0007167	0.57	enzyme linked receptor protein signaling pathway
GO:0051171	0.54	regulation of nitrogen compound metabolic process
GO:0031326	0.54	regulation of cellular biosynthetic process
GO:0010468	0.54	regulation of gene expression
GO:0007178	0.53	transmembrane receptor protein serine/threonine kinase signaling pathway
GO:0006355	0.53	regulation of transcription, DNA-templated
GO:0009893	0.51	positive regulation of metabolic process
GO:0031325	0.50	positive regulation of cellular metabolic process
GO:0010604	0.50	positive 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:0016020	0.83	membrane
GO:0044464	0.82	cell part
GO:0044424	0.57	intracellular part
GO:0005623	0.54	cell

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	3ij3A	0.450	5.90	0.063	0.862	3.4.11.1	129
2	0.060	2ptkA	0.443	4.19	0.175	0.603	2.7.10.2 2.7.1.112	NA
3	0.060	3c51B	0.459	3.74	0.133	0.581	2.7.11.14	NA
4	0.060	1l8aA	0.475	5.11	0.021	0.805	1.2.4.1	NA
5	0.060	2fo0A	0.469	3.60	0.127	0.603	2.7.10.2	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	0.88	1py5A	0.447	1.64	0.940	0.477	1.23	PY1	complex1.pdb.gz	103,111,122,123,124,152,170,172,173,174
2	0.62	3q4uC	0.437	1.55	0.683	0.471	0.84	LDN	complex2.pdb.gz	103,111,122,152
3	0.40	1b6c1	0.565	1.80	0.898	0.621	1.41	III	complex3.pdb.gz	86,87,88,90,91,92,134,135,138,139,142,143,157,159
4	0.12	3c51A	0.458	3.87	0.147	0.586	0.85	ADP	complex4.pdb.gz	103,105,106,111,122,124
5	0.03	2hz4C	0.389	1.82	0.187	0.431	1.00	4ST	complex5.pdb.gz	116,119,153,155

	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.