D-I-TASSER P35968-D2

D-I-TASSER results for P35968-D2

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

Input Sequence in FASTA format

>P35968 (216 residues)
EVSERDTGNYTVILTNPISKEKQSHVVSLVVYVPPQIGEKSLISPVDSYQYGTTQTLTCT
VYAIPPPHHIHWYWQLEEECANEPSQAVSVTNPYPCEEWRSVEDFQGGNKIEVNKNQFAL
IEGKNKTVSTLVIQAANVSALYKCEAVNKVGRGERVISFHVTRGPEITLQPDMQPTEQES
VSLWCTADRSTFENLTWYKLGPQPLPIHVGELPTPV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| EVSERDTGNYTVILTNPISKEKQSHVVSLVVYVPPQIGEKSLISPVDSYQYGTTQTLTCTVYAIPPPHHIHWYWQLEEECANEPSQAVSVTNPYPCEEWRSVEDFQGGNKIEVNKNQFALIEGKNKTVSTLVIQAANVSALYKCEAVNKVGRGERVISFHVTRGPEITLQPDMQPTEQESVSLWCTADRSTFENLTWYKLGPQPLPIHVGELPTPV
Prediction	CCCHHHCSSSSSSSSSCCCSSSSSSSSSSSSSCCCCCCCCCCCCCCSSSSCCCCSSSSSSSSCCCCCCSSSSSSCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCSSSSSCCSSSSSCCCCSSSSSSSSSCCCCCSSSSSSSSSCCCSSSSSSSSSSSCCCSSSSCCCCSSSCCCSSSSSSSSSSCCCCSSSSSSCCCCCCCCCCCCSCCCC
Confidence	998576769999999788618999999999831993233356787528837930999999873699828999973888765565420113665344454202223477167760543898638742788999815433689999999538717899999995598598358737857920999999971079879999789930667775345799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| EVSERDTGNYTVILTNPISKEKQSHVVSLVVYVPPQIGEKSLISPVDSYQYGTTQTLTCTVYAIPPPHHIHWYWQLEEECANEPSQAVSVTNPYPCEEWRSVEDFQGGNKIEVNKNQFALIEGKNKTVSTLVIQAANVSALYKCEAVNKVGRGERVISFHVTRGPEITLQPDMQPTEQESVSLWCTADRSTFENLTWYKLGPQPLPIHVGELPTPV
Prediction	844562544433334164354434130303030304035543355544144445040303043424133020314466424444443344443243543442444443230433443221344443211203144463413020202132344423030204320504343654334445040314052423040453256653143763524336
	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                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHCSSSSSSSSSCCCSSSSSSSSSSSSSCCCCCCCCCCCCCCSSSSCCCCSSSSSSSSCCCCCCSSSSSSCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCSSSSSCCSSSSSCCCCSSSSSSSSSCCCCCSSSSSSSSSCCCSSSSSSSSSSSCCCSSSSCCCCSSSCCCSSSSSSSSSSCCCCSSSSSSCCCCCCCCCCCCSCCCC
EVSERDTGNYTVILTNPISKEKQSHVVSLVVYVPPQIGEKSLISPVDSYQYGTTQTLTCTVYAIPPPHHIHWYWQLEEECANEPSQAVSVTNPYPCEEWRSVEDFQGGNKIEVNKNQFALIEGKNKTVSTLVIQAANVSALYKCEAVNKVGRGERVISFHVTRGPEITLQPDMQPTEQESVSLWCTADRSTFENLTWYKLGPQPLPIHVGELPTPV

2wngA

0.08

0.07

2.70

1.00

DEthreader

-VAAGESAILHTTVS-K-RENMDFSITELSVRAKPSAPVVSGP-A-ARATPQHTVSFTCESHGFSRDITLKWFKN-----------------------GN-E-------LSDFQ-TNVDPVSVSYSIHSTAKVVLTREDSQVICEVAHVTLPLRGTANLSIRVPPTL-EVTQQPVAENQVNVTCQVRKFYPQRLQLTWLENGNVSRTETASTVWMS

5t89X

0.36

0.33

9.79

1.35

SPARKS-K

DVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYAVSSFPDPALYPLGSRQILTCTAYGIPQP-TIKWFWHPCNEESFILDA-----------------DSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQK

5t89X

0.36

0.33

9.79

1.60

FFAS-3D

DVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYAVSSFPDPALYPLGSRQILTCTAYGIPQP-TIKWFWHPCNEESFILD-----------------ADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQ-

5t89X

0.36

0.32

9.66

2.86

CNFpred

DVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEVSSFPDPALYPLGSRQILTCTAYGIPQ-PTIKWFWHPCN------------------ESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQK

5o5gA

0.19

0.15

4.79

1.00

DEthreader

EYTRKSDAGKYVCVGT-NMVGERESVAELTVLERPSFVKRPS---NLAVTVDDSAEFKCEARGDPVP-TVRWRKDD----------------------GE-L-----PKSRYEIRD-----------DHTLKIRVTAGMGSYTCVAENMVGKAEASATLTVQEPPHFVVKPRDQVVALRTVTFQCEATGNPQPAIFWRREGSQNL-LFSYVSQTGD

4liqE

0.17

0.14

4.57

1.28

SPARKS-K

QVDFQHAGNYSCVASNVQG--KHSTSMFFRVVESAYLNLSSEQNLIQEVTVGEGLNLKVMVEAYPGLQGFNWTYLGPFSDHQPEK---------------------------------LANATTYRHTFTLSLPRLKEAGRYSFLARNPGGWRALTFELTLRYPPEVSVIWTFING---SGTLLCAASGYPQPNVTWLQCSGHTDRCDEAQVLQVW

5t89X

0.37

0.33

9.76

0.89

MapAlign

-VTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKSSFPDPALYPLGSRQILTCTAYGIPQPT-IKWFWHPC-------------------NEESFILDSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVNGFHVNLEKMPTEGEDLKLSCTVNSITLGTYACARNVYTGEEILQKKE----

5oyjC

0.97

0.71

19.86

0.69

CEthreader

EVSERDTGNYTVILTNPISKEKQSHVVSLVVYVPPQIGEKSLISPVDSYQYGTTQTLTCTVYAIPPPHHIHWYWQLEEECANENP--------YPCEEWRSVEDFQGGNKIEVNKNQFALIEGKNKTVSTLVIQAANVSALYKCEAVNKVGRGERVISFHVTRHHH--------------------------------------------------

5oyjC

0.97

0.71

19.86

0.93

MUSTER

EVSERDTGNYTVILTNPISKEKQSHVVSLVVYVPPQIGEKSLISPVDSYQYGTTQTLTCTVYAIPPPHHIHWYWQLEEECA--------NENPYPCEEWRSVEDFQGGNKIEVNKNQFALIEGKNKTVSTLVIQAANVSALYKCEAVNKVGRGERVISFHVTRHHH--------------------------------------------------

5t89X

0.28

0.27

8.36

0.59

HHsearch

KMQNKDKGLYTCRVRSGPSF--KSVNTSVHIYDKAFITVKHRKQQVLETVAGKRYRLSMKVKAFPSPE-VVWLKDGLPATEKSADVTEEDAGNYTILLSIKQSDSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSIINLT

(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	0.7412

(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	5t89X	0.81	2.28	0.362	0.907	model1_5t89X.pdb.gz
2	5oyjC	0.63	2.60	0.956	0.718	model1_5oyjC.pdb.gz
3	4bsjA	0.63	2.40	0.471	0.699	model1_4bsjA.pdb.gz
4	2nziA	0.57	4.02	0.124	0.745	model1_2nziA.pdb.gz
5	3b43A	0.56	4.18	0.186	0.768	model1_3b43A.pdb.gz
6	1qz1A	0.56	4.28	0.147	0.773	model1_1qz1A.pdb.gz
7	2wngA	0.56	4.36	0.131	0.768	model1_2wngA.pdb.gz
8	2wimA	0.55	4.10	0.139	0.759	model1_2wimA.pdb.gz
9	3f8uD	0.55	4.56	0.070	0.787	model1_3f8uD.pdb.gz
10	6iaaA	0.54	3.34	0.167	0.662	model1_6iaaA.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:0016773	0.94	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.94	kinase activity
GO:0004713	0.93	protein tyrosine kinase activity
GO:0004872	0.89	receptor activity
GO:0004871	0.89	signal transducer activity
GO:0019838	0.88	growth factor binding
GO:0005021	0.88	vascular endothelial growth factor-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:0065007	0.95	biological regulation
GO:0009987	0.94	cellular process
GO:0050789	0.92	regulation of biological process
GO:0044699	0.92	single-organism process
GO:0044767	0.90	single-organism developmental process
GO:0050794	0.81	regulation of cellular process
GO:0007165	0.75	signal transduction
GO:0007166	0.74	cell surface receptor signaling pathway
GO:0051239	0.73	regulation of multicellular organismal process
GO:0007169	0.73	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0044763	0.72	single-organism cellular process
GO:0008152	0.72	metabolic process
GO:0071704	0.71	organic substance metabolic process
GO:0044238	0.70	primary metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0043170	0.70	macromolecule metabolic process
GO:0048518	0.69	positive regulation of biological process
GO:0048010	0.69	vascular endothelial growth factor receptor signaling pathway
GO:0044260	0.69	cellular macromolecule metabolic process
GO:0048522	0.68	positive regulation of cellular process
GO:0050896	0.66	response to stimulus
GO:0042221	0.65	response to chemical
GO:0080090	0.64	regulation of primary metabolic process
GO:0070887	0.64	cellular response to chemical stimulus
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0048856	0.64	anatomical structure development
GO:0031323	0.64	regulation of cellular metabolic process
GO:0010033	0.64	response to organic substance
GO:0006464	0.64	cellular protein modification process
GO:0006468	0.63	protein phosphorylation
GO:0031325	0.62	positive regulation of cellular metabolic process
GO:0010604	0.62	positive regulation of macromolecule metabolic process
GO:0042325	0.61	regulation of phosphorylation
GO:0031399	0.61	regulation of protein modification process
GO:0048583	0.60	regulation of response to stimulus
GO:0035924	0.60	cellular response to vascular endothelial growth factor stimulus
GO:0001934	0.60	positive regulation of protein phosphorylation
GO:0046777	0.59	protein autophosphorylation
GO:0009966	0.59	regulation of signal transduction
GO:0009653	0.59	anatomical structure morphogenesis
GO:0048646	0.58	anatomical structure formation involved in morphogenesis
GO:0022603	0.58	regulation of anatomical structure morphogenesis
GO:0001525	0.57	angiogenesis
GO:0018108	0.56	peptidyl-tyrosine phosphorylation
GO:1902531	0.54	regulation of intracellular signal transduction
GO:0051240	0.54	positive regulation of multicellular organismal process
GO:0048584	0.54	positive regulation of response to stimulus
GO:0043410	0.53	positive regulation of MAPK cascade
GO:0040012	0.53	regulation of locomotion
GO:0032879	0.53	regulation of localization
GO:0030335	0.52	positive regulation of cell migration

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:0044464	0.99	cell part
GO:0044424	0.91	intracellular part
GO:0043226	0.74	organelle
GO:0043227	0.73	membrane-bounded organelle
GO:0044444	0.68	cytoplasmic part
GO:0043229	0.66	intracellular organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0016020	0.61	membrane
GO:0005886	0.58	plasma membrane
GO:0044425	0.57	membrane part
GO:0030054	0.55	cell junction
GO:0016021	0.55	integral component of membrane
GO:0005887	0.54	integral component of 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	0.060	3gm8A	0.423	4.71	0.070	0.625	3.2.1.-	NA
2	0.060	1zvhA	0.398	2.77	0.178	0.463	3.2.1.17	151,153
3	0.060	1wd9A	0.466	5.39	0.050	0.764	3.5.3.15	NA
4	0.060	3ejjX	0.458	4.18	0.095	0.662	2.7.10.1	NA
5	0.060	2c9aA	0.279	4.94	0.018	0.426	3.1.3.48	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	0.03	3qd1X	0.532	4.13	0.088	0.722	0.43	NA	complex1.pdb.gz	187,188,190,194
2	0.01	3qe5B	0.474	4.95	0.085	0.750	0.40	CA	complex2.pdb.gz	163,164,166
3	0.01	3k71G	0.477	4.86	0.051	0.736	0.58	CA	complex3.pdb.gz	165,166,188,190

	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.