D-I-TASSER P06865-D1

D-I-TASSER results for P06865-D1

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

Input Sequence in FASTA format

>P06865 (163 residues)
MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSV
LDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTI
NDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIED

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIED
Prediction	CCHHHHHHHHHHHHHHCCCCCCCCCCCCSSSSCCCSSSSCCCCSSSSSCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCCCCCCCCCSSSSSCCCCSSSSSCCHHHHHHHHHHHHHHHSSCCCCCSSSCSSSSSC
Confidence	9538999999999751477787568373899659719983782799983577667621799999999999997415877765456556655417999993589654667899963899983991899987678999999999998255599858982079729
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIED
Prediction	4431201000000003326421002233414347530302354040324354544443520440043025202545424444454554444432030304365465315374424040405574030304122002113100110033376221304505168
	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

CCHHHHHHHHHHHHHHCCCCCCCCCCCCSSSSCCCSSSSCCCCSSSSSCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCCCCCCCCCCCSSSSSCCCCSSSSSCCHHHHHHHHHHHHHHHSSCCCCCSSSCSSSSSC
MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIED

6yhhA1

0.21

0.17

5.47

1.17

DEthreader

-------MQKEQL-------NLMP-WPQNVVVNDGNFTLT-KNFKVNIS--GNP--DS-RIFGGVTRFLRRLDGRTGFFEQIKLNEFPNA---ELQINCTK--N-GKIGLYEDESYSLDVKANKITINATSDLGALHGLETLLQLLQNDSK-KFYFPVSQISD

6yhhA1

0.23

0.20

6.15

2.22

SPARKS-K

--------------QMQKEQLNLMPWPQNVVVNDGNFTLTKN-FKVNISGN-----PDSRIFGGVTRFLRRLDGRTGIFFEQGFITKLNEFPAELQINCTKNGKIG---LYEDESYSLDVKANKITINATSDLGALHGLETLLQLLQND-SKKFYFPVSQISD

3gh7A

0.17

0.15

5.02

1.13

MapAlign

---------VPRGSHMATSQPSILPKPVSYTVGSGQFVLTK-NASIFVAG--NNVGETDELFNIGQALAKKLNASTGYTISVVKS--NQPTAGSIYLTTVGGNA-----ALGNEGYDLITTSNQVTLTANKPEGVFRGNQTLLQLLPIVSGVQWVIPHSNISD

6yhhA1

0.24

0.20

6.32

0.90

CEthreader

--------------QMQKEQLNLMPWPQNVVVNDGNFTL-TKNFKVNISGN-----PDSRIFGGVTRFLRRLDGRTGIFFEQGFIKLNEFPNAELQINCTKNG---KIGLYEDESYSLDVKANKITINATSDLGALHGLETLLQLLQNDS-KKFYFPVSQISD

2gjxA1

0.98

0.76

21.32

1.95

MUSTER

----------------------LWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLDEAFQRYRDLLFGTLE--------------KNVLVVSVVTPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIED

3nsmA1

0.19

0.18

5.75

2.23

HHsearch

NDPSEPALSLEACKMFCNEYGLLWPRPTGEDLGNFLSKINLNSIEVKILKK---GATDDLMEAAAKRFKEQVSLAIPRGSTPK------LTGKAVDVYVNENPNEKAFSLEMDESYGLRVSPSNATITANSFFGMRHGLETLSQLFVFDDIHLLMVRDVNISD

2gjxA1

0.99

0.77

21.65

1.89

FFAS-3D

----------------------LWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSVLDEAFQRYRDLLFGT--------------LEKNVLVVSVVTPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIED

6yhhA1

0.21

0.18

5.65

1.22

EigenThreader

--------------QMQKEQLNLMPWPQNVVVNDGNFTLTKNFKVNISGN------PDSRIFGGVTRFLRRLDGRTGIFFEQITKLNEFPNAELQINCTKNGKIGLYE----DESYSLDVKANKITINATSDLGALHGLETLLQLLQNDS-KKFYFPVSQISD

5y0vA

0.18

0.17

5.37

1.85

CNFpred

-------LSLEACKMFCNEYGLLWPRPTGADLGNFLSKINLNSIEVKILKKG---ATDDLMEAAAKRFKEQVSLAIPRGSTPKL------TGKAVDVYLVNEPNEKAFSLEMDESYGLRVSPVNATITANSFFGMRHGLETLSQLFVFDDDHLLMVRDVNISD

6yhhA

0.21

0.17

5.47

1.17

DEthreader

-------MQKEQL-------NLMP-WPQNVVVNDGNFTLT-KNFKVNIS--GNP--DS-RIFGGVTRFLRRLDGRTGFFEQITKLNEFPNA--ELQINCTK--N-GKIGLYEDESYSLDVKANKITINATSDLGALHGLETLLQLLQNDSK-KFYFPVSQISD

(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	0.748

(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	2gjxA1	0.77	0.45	0.913	0.773	model1_2gjxA1.pdb.gz
2	1o7aA1	0.76	1.03	0.422	0.785	model1_1o7aA1.pdb.gz
3	3nsmA1	0.72	2.75	0.155	0.847	model1_3nsmA1.pdb.gz
4	3gh7A	0.60	3.11	0.158	0.742	model1_3gh7A.pdb.gz
5	1m04A	0.56	3.17	0.134	0.706	model1_1m04A.pdb.gz
6	2v5dA	0.56	3.00	0.173	0.681	model1_2v5dA.pdb.gz
7	2chnA1	0.51	2.59	0.204	0.607	model1_2chnA1.pdb.gz
8	1qbaA3	0.35	5.08	0.042	0.583	model1_1qbaA3.pdb.gz
9	3pqsA1	0.32	5.43	0.033	0.583	model1_3pqsA1.pdb.gz
10	4lxrA	0.27	5.12	0.081	0.442	model1_4lxrA.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:0004563	1.00	beta-N-acetylhexosaminidase activity
GO:0046983	0.76	protein dimerization activity
GO:0046982	0.75	protein heterodimerization activity
GO:0016740	0.75	transferase activity
GO:0016758	0.73	transferase activity, transferring hexosyl groups
GO:0008194	0.72	UDP-glycosyltransferase activity
GO:0008375	0.65	acetylglucosaminyltransferase 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:0044699	0.88	single-organism process
GO:0008152	0.79	metabolic process
GO:0071704	0.77	organic substance metabolic process
GO:0009987	0.69	cellular process
GO:0044238	0.67	primary metabolic process
GO:1901135	0.62	carbohydrate derivative metabolic process
GO:0044710	0.62	single-organism metabolic process
GO:0044763	0.61	single-organism cellular process
GO:0044237	0.61	cellular metabolic process
GO:0043170	0.59	macromolecule metabolic process
GO:0006807	0.59	nitrogen compound metabolic process
GO:1901564	0.56	organonitrogen compound metabolic process
GO:0032502	0.56	developmental process
GO:0044767	0.55	single-organism developmental process
GO:1901575	0.53	organic substance catabolic process
GO:0006629	0.53	lipid metabolic process
GO:0044255	0.52	cellular lipid metabolic process
GO:0006022	0.52	aminoglycan metabolic process
GO:1901565	0.51	organonitrogen compound catabolic process
GO:1901136	0.51	carbohydrate derivative catabolic process
GO:0044248	0.51	cellular catabolic process
GO:0006687	0.51	glycosphingolipid metabolic process
GO:0030203	0.50	glycosaminoglycan 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:0044464	0.97	cell part
GO:0044424	0.94	intracellular part
GO:0044444	0.90	cytoplasmic part
GO:0043227	0.89	membrane-bounded organelle
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0005773	0.85	vacuole
GO:0005764	0.79	lysosome
GO:0044421	0.74	extracellular region part
GO:0016020	0.74	membrane
GO:0070062	0.64	extracellular exosome
GO:0042582	0.62	azurophil granule
GO:0044422	0.51	organelle part
GO:0044446	0.50	intracellular organelle part

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	2nyaA	0.420	4.90	0.060	0.724	1.7.99.4	NA
2	0.060	1ks0A	0.152	4.21	0.053	0.239	3.4.24.24	129
3	0.060	1q50A	0.412	4.68	0.057	0.650	5.3.1.9	NA
4	0.060	1j7mA	0.162	4.52	0.033	0.264	3.4.24.24	100,102
5	0.060	1slmA	0.462	4.48	0.047	0.706	3.4.24.17	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	0.32	2gk1G	0.765	0.49	0.913	0.773	0.35	UUU	complex1.pdb.gz	24,25,140
2	0.24	1np0A	0.754	1.01	0.425	0.779	0.13	NGT	complex2.pdb.gz	132,140,142
3	0.22	1nowA	0.754	1.01	0.425	0.779	0.21	IFG	complex3.pdb.gz	129,138,145,159
4	0.11	2cbiB	0.559	3.01	0.173	0.681	0.36	GBL	complex4.pdb.gz	95,128,132,139
5	0.06	2jiwA	0.515	2.87	0.188	0.632	0.14	BEU	complex5.pdb.gz	115,138,141
6	0.05	2cbjB	0.558	3.02	0.172	0.681	0.37	OAN	complex6.pdb.gz	134,138,139
7	0.04	2vurA	0.559	3.02	0.173	0.681	0.11	YX1	complex7.pdb.gz	26,113,141
8	0.01	1d5jB	0.425	4.11	0.065	0.607	0.39	MM3	complex8.pdb.gz	134,137,138,141
9	0.01	2j47A	0.283	4.85	0.014	0.485	0.14	GDV	complex9.pdb.gz	127,138,144,145
10	0.01	2usnA	0.422	4.05	0.052	0.601	0.30	IN8	complex10.pdb.gz	116,133,134,137

	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.