D-I-TASSER Q08629-D2

D-I-TASSER results for Q08629-D2

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

Input Sequence in FASTA format

>Q08629 (173 residues)
CKPCPVAQSAMVCGSDGHSYTSKCKLEFHACSTGKSLATLCDGPCPCLPEPEPPKHKAER
SACTDKELRNLASRLKDWFGALHEDANRVIKPTSSNTAQGRFDTSILPICKDSLGWMFNK
LDMNYDLLLDPSEINAIYLDKYEPCIKPLFNSCDSFKDGKLSNNEWCYCFQKP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| CKPCPVAQSAMVCGSDGHSYTSKCKLEFHACSTGKSLATLCDGPCPCLPEPEPPKHKAERSACTDKELRNLASRLKDWFGALHEDANRVIKPTSSNTAQGRFDTSILPICKDSLGWMFNKLDMNYDLLLDPSEINAIYLDKYEPCIKPLFNSCDSFKDGKLSNNEWCYCFQKP
Prediction	CCCCCCCCCCCCCCCCCCSCCCSSSSSHHHHHCCCSCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCSCHHHHHHHHCCC
Confidence	97999899986458899061643566433554397211222687544444333445433332102347888999999999998754311455534331011222202467789999999848899998699999987521125789999997158999862899999997489
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| CKPCPVAQSAMVCGSDGHSYTSKCKLEFHACSTGKSLATLCDGPCPCLPEPEPPKHKAERSACTDKELRNLASRLKDWFGALHEDANRVIKPTSSNTAQGRFDTSILPICKDSLGWMFNKLDMNYDLLLDPSEINAIYLDKYEPCIKPLFNSCDSFKDGKLSNNEWCYCFQKP
Prediction	85715666543010334432403030233323454504443444534444454444444344345432540342034124314534544444454454454355533542444034204411443234024620451444444510440073015353340025002501758
	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

CCCCCCCCCCCCCCCCCCSCCCSSSSSHHHHHCCCSCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCSCHHHHHHHHCCC
CKPCPVAQSAMVCGSDGHSYTSKCKLEFHACSTGKSLATLCDGPCPCLPEPEPPKHKAERSACTDKELRNLASRLKDWFGALHEDANRVIKPTSSNTAQGRFDTSILPICKDSLGWMFNKLDMNYDLLLDPSEINAIYLDKYEPCIKPLFNSCDSFKDGKLSNNEWCYCFQKP

1bmoA

0.16

0.13

4.42

1.00

DEthreader

GQDPTS-----KVCSNDNKT-FDS-HFKK-KLHLDYIGPC-------------------PPCLD-SELTEFPLRMRDWLKNVLVTLYEDKLR--KKIHENEKRDKNYNMYIFPVHWQFGQLDQPIDGYLSHTELAPLRAPLIEHCTTRFFETCDLDNDKYIALDEWAGCFGIK

1bmoA

0.24

0.23

7.01

2.21

SPARKS-K

CPA-PIGEFEKVCSNDNKTFDSSCHFFATKCTLEHKLHLDYIGPCK------------YIPPCLDSELTEFPLRMRDWLKNVLVTLYERDEDNNLHENEKRLEAGDHPVYIFPVHWQFGQLDQHIDGYLSHTELAPLRLIPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIK

1bmoA

0.23

0.22

6.87

1.29

MapAlign

QDPTSCPAPEKVCSNDNKTFDSSCHFFATLEGTKKGHKLHLDYIGPCK----------YIPPCLDSELTEFPLRMRDWLKNVLVTLYERDEDNNLLTELARDFEKNYNMYIFPVHWQFGQLDQHPDGYLSHTELAPLRLIPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIK

1bmoA

0.24

0.23

7.02

0.95

CEthreader

PTSCPAPEFEKVCSNDNKTFDSSCHFFATKCTLGHKLHLDYIGPCKY------------IPPCLDSELTEFPLRMRDWLKNVLVTLYERDEDNNLLTEKQKLRVKKIHMYIFPVHWQFGQLDQHIDGYLSHTELAPLRLIPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIK

1bmoA

0.24

0.22

6.86

1.51

MUSTER

CPA-PIGEFEKVCSNDNKTFDSSCHFFATKCTLEGTLHLDYIGPCKYIPP------------CLDSELTEFPLRMRDWLKNVLVTLYERDEDNNLVKKIHENEKRLEAGYIFPVHWQFGQLDQHIDGYLSHTELAPLPLIPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIK

1bmoA

0.25

0.23

7.17

2.43

HHsearch

PTSCPAPEFEKVCSNDNKTFDSSCHFFATKCTLGHKLHLDYIGPCKY------------IPPCLDSELTEFPLRMRDWLKNVLVTLYRDEDNNLTEKQEKRLLEKNYNMYIFPVHWQFGQLDQHIDGYLSHTELAPLRLIPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIK

1bmoA

0.25

0.24

7.33

1.46

FFAS-3D

CCPAPIGEFEKVCSNDNKTFDSSCHFFATKCTLEGTLHLDYIGPCKYI------------PPCLDSELTEFPLRMRDWLKKIHENEKRLEAGDHPVELLARDFEKNYNMYIFPVHWQFGQLDQHPDGYLSHTELAPLRAPPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIK

7kbuA

0.21

0.19

6.06

0.78

EigenThreader

VTCPPTKPLDQVCGTDNQTYASSCHLFATKCRLEGTQLDYFGACKS-------------IPTCT---DFEVIQFPLRMRDWLKNDEKRLLAGDHPIDLLLRDFKKNYHMYVYPVHWQFSELDQHPMDRHSELAPLRASLVPMEHCITRFFEECDPNKDKHITLKEWGHCFGIK

1nubA

0.23

0.21

6.70

1.90

CNFpred

PTSCPAPIGEKVCSNDNKTFDSSCHFFATKCTLEHKLHLDYIGPCKYIP------------PCLDSELTEFPLRMRDWLKNVLVTLDNNLLTEKQKLRVKKIHE-NYNMYIFPVHWQFGQLDQHPDGYLSHTELAPLRAIPMEHCTTRFFETCDLDNDKYIALDEWAGCFGIK

1bmoA2

0.19

0.13

4.09

0.83

DEthreader

--------------YI------------------P------------------------PCLDS--ELTEFPLRMRDWLKNVLVTLYEDLTE--KLRVKKIHNKKNYNMYIFPVHWQFGQLDQPIDGYLSHTELAPLRAPIMEHCTTRFFETCDLDNDKYIALDEWAGCFGIK

(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	0.6857

(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	1bmoA	0.87	1.45	0.224	0.931	model1_1bmoA.pdb.gz
2	7kbuA	0.52	3.74	0.172	0.746	model1_7kbuA.pdb.gz
3	2aw3A	0.48	4.89	0.057	0.786	model1_2aw3A.pdb.gz
4	2amvA	0.48	5.04	0.054	0.798	model1_2amvA.pdb.gz
5	4bqeA	0.47	5.16	0.047	0.803	model1_4bqeA.pdb.gz
6	3godA	0.46	5.31	0.050	0.780	model1_3godA.pdb.gz
7	1ka1A	0.41	5.35	0.022	0.717	model1_1ka1A.pdb.gz
8	2htvA	0.39	5.30	0.058	0.670	model1_2htvA.pdb.gz
9	3ai1A	0.34	5.66	0.054	0.619	model1_3ai1A.pdb.gz
10	2p6aD3	0.33	4.05	0.169	0.457	model1_2p6aD3.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:0043167	0.90	ion binding
GO:0046872	0.89	metal ion binding
GO:0005509	0.88	calcium ion binding
GO:0004857	0.79	enzyme inhibitor activity
GO:0008191	0.78	metalloendopeptidase inhibitor activity
GO:0004869	0.73	cysteine-type endopeptidase inhibitor 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	0.95	single-organism process
GO:0009987	0.92	cellular process
GO:0065007	0.88	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0044763	0.87	single-organism cellular process
GO:0050794	0.84	regulation of cellular process
GO:0080090	0.73	regulation of primary metabolic process
GO:0060255	0.73	regulation of macromolecule metabolic process
GO:0048519	0.73	negative regulation of biological process
GO:0031323	0.73	regulation of cellular metabolic process
GO:0050790	0.72	regulation of catalytic activity
GO:0048523	0.72	negative regulation of cellular process
GO:0051336	0.71	regulation of hydrolase activity
GO:0032268	0.71	regulation of cellular protein metabolic process
GO:0051239	0.70	regulation of multicellular organismal process
GO:2000026	0.69	regulation of multicellular organismal development
GO:0051346	0.69	negative regulation of hydrolase activity
GO:0051128	0.69	regulation of cellular component organization
GO:0045595	0.69	regulation of cell differentiation
GO:0032269	0.69	negative regulation of cellular protein metabolic process
GO:0048869	0.68	cellular developmental process
GO:0010951	0.68	negative regulation of endopeptidase activity
GO:0010810	0.68	regulation of cell-substrate adhesion
GO:0051960	0.67	regulation of nervous system development
GO:0051241	0.67	negative regulation of multicellular organismal process
GO:0051093	0.67	negative regulation of developmental process
GO:0031344	0.67	regulation of cell projection organization
GO:0010975	0.65	regulation of neuron projection development
GO:0006928	0.65	movement of cell or subcellular component
GO:0022008	0.64	neurogenesis
GO:0021953	0.64	central nervous system neuron differentiation
GO:0010977	0.64	negative regulation of neuron projection development
GO:0010812	0.64	negative regulation of cell-substrate adhesion
GO:0001764	0.64	neuron 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:0044421	0.95	extracellular region part
GO:0044464	0.90	cell part
GO:0005615	0.89	extracellular space
GO:0044424	0.86	intracellular part
GO:0045202	0.77	synapse
GO:0005737	0.76	cytoplasm
GO:0033267	0.72	axon part
GO:0033268	0.71	node of Ranvier
GO:0031594	0.71	neuromuscular junction
GO:0016528	0.71	sarcoplasm

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	3b9jJ	0.328	5.89	0.027	0.624	1.17.1.4 1.17.3.2	30
2	0.060	2bjiA	0.417	5.10	0.014	0.682	3.1.3.25	NA
3	0.060	2aryA	0.353	5.62	0.077	0.613	3.4.22.52	NA
4	0.060	1s46A	0.424	5.34	0.043	0.734	2.4.1.4	20
5	0.060	1ofdA	0.396	6.07	0.043	0.763	1.4.7.1	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	0.05	1bmoA	0.870	1.45	0.224	0.931	0.54	CA	complex1.pdb.gz	16,18,20,41
	2	0.01	2gm9A	0.393	5.66	0.036	0.728	0.41	3TH	complex2.pdb.gz	15,44,132,133,134

	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.