D-I-TASSER Q8IUR5-D4

D-I-TASSER results for Q8IUR5-D4

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

Input Sequence in FASTA format

>Q8IUR5 (117 residues)
NHDKALDAIDKALQLKPKDPKVISELFFTKGNQLREQNLLDKAFESYRVAVQLNPDQAQA
WMNMGGIQHIKGKYVSARAYYERALQLVPDSKLLKENLAKLDRLEKRLQEVREKDQT

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| NHDKALDAIDKALQLKPKDPKVISELFFTKGNQLREQNLLDKAFESYRVAVQLNPDQAQAWMNMGGIQHIKGKYVSARAYYERALQLVPDSKLLKENLAKLDRLEKRLQEVREKDQT
Prediction	CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHCC
Confidence	899999999999981999848899999989999999099999999999999849999999988999999919999999999999983999999999999999990999999998539
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| NHDKALDAIDKALQLKPKDPKVISELFFTKGNQLREQNLLDKAFESYRVAVQLNPDQAQAWMNMGGIQHIKGKYVSARAYYERALQLVPDSKLLKENLAKLDRLEKRLQEVREKDQT
Prediction	836401610540060327344221301211010145375264016205400613272140121112014537526401620540061327224012110300543642640373378
	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

                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHCC
NHDKALDAIDKALQLKPKDPKVISELFFTKGNQLREQNLLDKAFESYRVAVQLNPDQAQAWMNMGGIQHIKGKYVSARAYYERALQLVPDSKLLKENLAKLDRLEKRLQEVREKDQT

1qz2A

0.19

6.08

1.50

DEthreader

KYKQALLQYKKIVSWLEAAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLFRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAREKKLYN

3pe3A1

0.26

0.25

7.66

1.46

SPARKS-K

NIEEAVRLYRKALEVFPEF----AAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRT

2fbnA

0.13

0.12

4.15

0.53

MapAlign

-INEAIVKYKEALDFFDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNKLKEAR--------

2fbnA

0.13

0.12

4.17

0.34

CEthreader

EINEAIVKYKEALDFFIKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNKLKEARK-------

6b85J

0.29

0.28

8.58

1.14

MUSTER

RLSLAAEAYKKAIELDPND----ALAWLLLGSVLEKLKRLDEAAEAYKKAIELKPNDASAWKELGKVLEKLGRLDEAAEAYKKAIELDPEDAEAWKELGKVLEKLGRLDEAAEAYKK

3pe3A

0.26

0.25

7.66

0.58

HHsearch

NIEEAVRLYRKALEVFPEFA----AAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRT

3pe3A1

0.25

0.24

7.42

2.01

FFAS-3D

NIEEAVRLYRKALEVFPEF----AAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYR-

6tedQ

0.15

5.15

0.53

EigenThreader

NLGEAKKYFLASLDRAKAEAAISVTTSYNLARLYEAMCEFHEAEKLYKNILREHPNYVDCYLRLGAMARDKGNFYEASDWFKEALQINQDHPDAWSLIGNLHLAYSMLALGNVWLQT

3cv0A

0.23

0.22

6.97

1.03

CNFpred

EYRECRTLLHAALEMNPN----DAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVR

1ihgA

0.17

5.61

1.50

DEthreader

NWEMAIKKYTKVLRYVERLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKDKEKAA-Y

(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	0.8655

(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	1ihgA	0.91	1.40	0.172	0.992	model1_1ihgA.pdb.gz
2	1qz2A	0.90	1.55	0.188	1.000	model1_1qz2A.pdb.gz
3	6hftA1	0.90	1.59	0.205	1.000	model1_6hftA1.pdb.gz
4	5jheA	0.89	1.41	0.167	0.974	model1_5jheA.pdb.gz
5	1kt1A	0.86	1.94	0.162	0.983	model1_1kt1A.pdb.gz
6	7kdtA	0.86	2.00	0.129	0.983	model1_7kdtA.pdb.gz
7	4a1sA	0.86	2.23	0.197	0.983	model1_4a1sA.pdb.gz
8	4i1aA	0.85	1.26	0.128	0.914	model1_4i1aA.pdb.gz
9	3uq3A	0.85	1.54	0.153	0.949	model1_3uq3A.pdb.gz
10	5l0wB	0.85	1.49	0.193	0.932	model1_5l0wB.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:0003824	0.76	catalytic activity
GO:0016740	0.64	transferase activity
GO:0036094	0.57	small molecule binding
GO:0042277	0.55	peptide binding
GO:0008375	0.54	acetylglucosaminyltransferase activity
GO:1901363	0.53	heterocyclic compound binding
GO:0097159	0.53	organic cyclic compound binding
GO:0034212	0.53	peptide N-acetyltransferase activity
GO:0016262	0.53	protein N-acetylglucosaminyltransferase activity
GO:0030234	0.50	enzyme regulator 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:0009987	0.97	cellular process
GO:0008152	0.79	metabolic process
GO:0071704	0.78	organic substance metabolic process
GO:0044699	0.77	single-organism process
GO:0044238	0.77	primary metabolic process
GO:0044237	0.77	cellular metabolic process
GO:0044260	0.76	cellular macromolecule metabolic process
GO:0044763	0.73	single-organism cellular process
GO:0065007	0.71	biological regulation
GO:0050789	0.69	regulation of biological process
GO:0050794	0.68	regulation of cellular process
GO:0016043	0.68	cellular component organization
GO:0019538	0.63	protein metabolic process
GO:0044267	0.62	cellular protein metabolic process
GO:0043412	0.62	macromolecule modification
GO:0006464	0.61	cellular protein modification process
GO:0051179	0.60	localization
GO:0032502	0.60	developmental process
GO:0080090	0.59	regulation of primary metabolic process
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:0044767	0.59	single-organism developmental process
GO:0031323	0.59	regulation of cellular metabolic process
GO:0022607	0.59	cellular component assembly
GO:0048518	0.57	positive regulation of biological process
GO:0043933	0.57	macromolecular complex subunit organization
GO:0051641	0.56	cellular localization
GO:0050896	0.56	response to stimulus
GO:0048522	0.56	positive regulation of cellular process
GO:0044710	0.56	single-organism metabolic process
GO:0010468	0.56	regulation of gene expression
GO:0009889	0.56	regulation of biosynthetic process
GO:0006996	0.56	organelle organization
GO:2000112	0.55	regulation of cellular macromolecule biosynthetic process
GO:0065003	0.55	macromolecular complex assembly
GO:0051252	0.55	regulation of RNA metabolic process
GO:0051128	0.54	regulation of cellular component organization
GO:0048856	0.54	anatomical structure development
GO:0048523	0.54	negative regulation of cellular process
GO:0044707	0.54	single-multicellular organism process
GO:0032268	0.54	regulation of cellular protein metabolic process
GO:0031325	0.54	positive regulation of cellular metabolic process
GO:0010604	0.54	positive regulation of macromolecule metabolic process
GO:0007165	0.54	signal transduction
GO:0006355	0.54	regulation of transcription, DNA-templated
GO:0048583	0.53	regulation of response to stimulus
GO:0033043	0.53	regulation of organelle organization
GO:0018193	0.53	peptidyl-amino acid modification
GO:0006493	0.53	protein O-linked glycosylation
GO:0051254	0.52	positive regulation of RNA metabolic process
GO:0033044	0.52	regulation of chromosome organization
GO:0031399	0.52	regulation of protein modification process
GO:0010628	0.52	positive regulation of gene expression
GO:0009892	0.52	negative regulation of metabolic process
GO:0006473	0.52	protein acetylation
GO:0065008	0.51	regulation of biological quality
GO:0051716	0.51	cellular response to stimulus
GO:0045893	0.51	positive regulation of transcription, DNA-templated
GO:0042221	0.51	response to chemical
GO:0032270	0.51	positive regulation of cellular protein metabolic process
GO:0031324	0.51	negative regulation of cellular metabolic process
GO:0031060	0.51	regulation of histone methylation
GO:0010605	0.51	negative regulation of macromolecule metabolic process
GO:0009966	0.51	regulation of signal transduction
GO:0009605	0.51	response to external stimulus
GO:0006461	0.51	protein complex assembly
GO:0006357	0.51	regulation of transcription from RNA polymerase II promoter
GO:0006325	0.51	chromatin organization
GO:0051640	0.50	organelle localization
GO:0050793	0.50	regulation of developmental process
GO:0045944	0.50	positive regulation of transcription from RNA polymerase II promoter
GO:0043414	0.50	macromolecule methylation
GO:0043207	0.50	response to external biotic stimulus
GO:0042325	0.50	regulation of phosphorylation
GO:0035556	0.50	intracellular signal transduction
GO:0031401	0.50	positive regulation of protein modification process
GO:0031400	0.50	negative regulation of protein modification process
GO:0010638	0.50	positive regulation of organelle organization
GO:0010033	0.50	response to organic substance
GO:0009894	0.50	regulation of catabolic 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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0043226	0.84	organelle
GO:0044446	0.83	intracellular organelle part
GO:0043229	0.82	intracellular organelle
GO:0043231	0.79	intracellular membrane-bounded organelle
GO:0044444	0.76	cytoplasmic part
GO:0032991	0.56	macromolecular complex
GO:0016020	0.56	membrane
GO:0005634	0.56	nucleus
GO:0043234	0.50	protein complex
GO:0005829	0.50	cytosol

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	0.245	1tjcA	0.679	1.91	0.136	0.752	1.14.11.2	28
2	0.244	2fbnA	0.808	1.83	0.118	0.940	5.2.1.8	NA
3	0.092	1klxA	0.569	2.77	0.144	0.744	3.5.2.6	80
4	0.060	2if4A	0.718	2.41	0.112	0.829	5.2.1.8	NA
5	0.060	1ihgA	0.909	1.40	0.172	0.992	5.2.1.8	98

	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	0.53	1elrA	0.783	1.53	0.204	0.880	1.12	III	complex1.pdb.gz	28,32,35,38,47,59,63,66,69,70,93,97,100
	2	0.16	2xcbA	0.793	1.36	0.137	0.872	1.20	III	complex2.pdb.gz	25,28,29,32,35,63,66,93,97

	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.