D-I-TASSER A8MYJ7-D5

D-I-TASSER results for A8MYJ7-D5

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

Input Sequence in FASTA format

>A8MYJ7 (163 residues)
GQPRQALGYCSLSVLASGSSACHLRLRATCLAELQEFGRALRDLDHVLQEALGDGDLPRR
AEDFCRQGRLLLSLGDEAAAAGAFAQALKLAPSLAQNSLCRQPGRAPTARMFLLRGQCCL
EEQRHAEAWTAVESGLLVDPDHRGLKRLKARIRREASSGCWLQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GQPRQALGYCSLSVLASGSSACHLRLRATCLAELQEFGRALRDLDHVLQEALGDGDLPRRAEDFCRQGRLLLSLGDEAAAAGAFAQALKLAPSLAQNSLCRQPGRAPTARMFLLRGQCCLEEQRHAEAWTAVESGLLVDPDHRGLKRLKARIRREASSGCWLQ
Prediction	CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCC
Confidence	9899999999999985999899999999999998489999999999996188886324789999999999999099999999999999849863677887321036999999999999999788999999999999879899999999999997741366559
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| GQPRQALGYCSLSVLASGSSACHLRLRATCLAELQEFGRALRDLDHVLQEALGDGDLPRRAEDFCRQGRLLLSLGDEAAAAGAFAQALKLAPSLAQNSLCRQPGRAPTARMFLLRGQCCLEEQRHAEAWTAVESGLLVDPDHRGLKRLKARIRREASSGCWLQ
Prediction	8536401620240062247214101210300430561650160034006234745513530430032020133155165016004400611373332214544444411420252044125474154015103300410372450341324053426450447
	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

CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCC
GQPRQALGYCSLSVLASGSSACHLRLRATCLAELQEFGRALRDLDHVLQEALGDGDLPRRAEDFCRQGRLLLSLGDEAAAAGAFAQALKLAPSLAQNSLCRQPGRAPTARMFLLRGQCCLEEQRHAEAWTAVESGLLVDPDHRGLKRLKARIRREASSGCWLQ

3sf4A

0.16

0.15

4.90

1.33

DEthreader

GNFRDAVIAHEQRLLIAKKERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQLNDRI---------GEGRACWSLGNAYTALGNHDQAMHFAEKHLEISRKELTARLNLSDLQMVLGLSY---

4ui9C3

0.08

0.07

2.70

1.44

SPARKS-K

SMKSELSYLAHNLCEIDKYRVETCCVIGNYYSLRSQHEKAALYFQRALKLNPR------YLGAWTLMGHEYMEMKNTSAAIQAYRHAIEVNKRDY--------------RAWYGLGQTYEILKMPFYCLYYYRRAHQLRPNDSRMLVALGECYEKLNQLVEAK

3uq3A

0.16

5.29

0.47

MapAlign

RQFDEAIEHYNKAWELH-KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRAYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTEHTADILTKLRMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVKEYASA-

4a1sA

0.15

0.14

4.76

0.31

CEthreader

EALTRAVEFYQENLKLMGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGE--------REVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELARACWSLGNAHSAIGGHERAL

5aemA1

0.10

0.09

3.17

1.34

MUSTER

NDLQVAERLFNEVIKKDARNFAAYETLGDIYQLQGRLNDCCNSWFLAAHLN------ASDWEFWKIVAILSADLDHVRQAIYCFSRVISLNPME--------------WESIYRRSMLYKKTGQLARALDGFQRLYMYNPYDANILRELAILYVDYDR-----

3pe3A

0.16

0.13

4.51

0.61

HHsearch

GNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPT------FADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFA--------------DAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCD--WTD

6vbu42

0.17

0.15

4.85

2.06

FFAS-3D

-DLDKAIEIYKKAVEFSPENTELLTTLGLLYLQLGIYQKAFEHLGNTLTYDPTACAVIESPPLWNNIGMCFFGKKKYVAAISCLKRANYLAPLDWKI--------------LYNLGLVHLTMQQYASAFHFLSAAINFQPKMGELYMLLAVALTNLED-----

3txmA

0.10

0.09

3.44

0.57

EigenThreader

AGTGIEVQLCKDCIEWAKQEQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAI-------YCPPKVQGALDLQSGILHAADEDFKTAFSYFYEAFEGFDSVDTSLKYMLLCKIMLGQSDDVN

4rg6A

0.12

4.10

1.13

CNFpred

REHDIAIKFFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNAIRVN------PRHYNAWYGLGMIYYKQEKFSLAEMHFQKALDINPQSSVLLCHIGV-DPKNPLCKFHRASVLFANEKYKSALQELEELKQIVPKESLVYFLIGKVYKKLGQTHLAL

4a1sA

0.13

0.12

4.23

1.33

DEthreader

VALTRAVEFYQENLKLMRRQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVLGERE---------VEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQREARACWSLGNAHSAIGG-----

(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	0.8233

(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	4a1sA	0.86	1.75	0.142	0.926	model1_4a1sA.pdb.gz
2	3sf4A	0.85	1.88	0.148	0.926	model1_3sf4A.pdb.gz
3	5o09C	0.81	2.33	0.127	0.926	model1_5o09C.pdb.gz
4	6mfvA	0.81	2.02	0.084	0.920	model1_6mfvA.pdb.gz
5	4nq0A	0.80	2.42	0.101	0.945	model1_4nq0A.pdb.gz
6	4i1aA	0.80	2.04	0.085	0.908	model1_4i1aA.pdb.gz
7	6tntJ	0.80	1.96	0.134	0.902	model1_6tntJ.pdb.gz
8	4xi0A	0.79	1.60	0.196	0.853	model1_4xi0A.pdb.gz
9	3cvnA	0.79	1.63	0.105	0.853	model1_3cvnA.pdb.gz
10	3ceqB	0.78	2.49	0.134	0.920	model1_3ceqB.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:0046872	1.00	metal ion binding
GO:1901363	0.62	heterocyclic compound binding
GO:0097159	0.62	organic cyclic compound binding
GO:0003824	0.61	catalytic activity
GO:0019899	0.55	enzyme binding
GO:0019904	0.54	protein domain specific binding
GO:1901265	0.51	nucleoside phosphate binding
GO:0050839	0.51	cell adhesion molecule binding
GO:0031267	0.51	small GTPase binding
GO:0098632	0.50	protein binding involved in cell-cell adhesion
GO:0045296	0.50	cadherin binding

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:0038061	1.00	NIK/NF-kappaB signaling
GO:0009987	0.83	cellular process
GO:0044699	0.66	single-organism process
GO:0044763	0.65	single-organism cellular process
GO:0016043	0.61	cellular component organization
GO:0044767	0.59	single-organism developmental process
GO:0051179	0.58	localization
GO:0051641	0.57	cellular localization
GO:1902578	0.55	single-organism localization
GO:0048869	0.54	cellular developmental process
GO:0048856	0.54	anatomical structure development
GO:0065008	0.52	regulation of biological quality
GO:0051234	0.52	establishment of localization
GO:0060429	0.51	epithelium development
GO:0051649	0.51	establishment of localization in cell
GO:0051640	0.51	organelle localization
GO:0051336	0.51	regulation of hydrolase activity
GO:0051235	0.51	maintenance of location
GO:0048468	0.51	cell development
GO:0043085	0.51	positive regulation of catalytic activity
GO:0030154	0.51	cell differentiation
GO:0061028	0.50	establishment of endothelial barrier
GO:0060479	0.50	lung cell differentiation
GO:0060428	0.50	lung epithelium development
GO:0051657	0.50	maintenance of organelle location
GO:0051642	0.50	centrosome localization
GO:0051345	0.50	positive regulation of hydrolase activity
GO:0045216	0.50	cell-cell junction organization
GO:0043087	0.50	regulation of GTPase activity
GO:0007155	0.50	cell adhesion

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:0005634	1.00	nucleus
GO:0044444	0.83	cytoplasmic part
GO:0005737	0.75	cytoplasm
GO:0044446	0.72	intracellular organelle part
GO:0043234	0.66	protein complex
GO:0016020	0.61	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	0.179	1tjcA	0.529	1.93	0.138	0.577	1.14.11.2	88
2	0.172	2fbnA	0.697	2.30	0.092	0.804	5.2.1.8	29
3	0.060	1hn0A	0.562	4.26	0.074	0.896	4.2.2.20	NA
4	0.060	2cqsA	0.579	4.04	0.056	0.853	2.4.1.20	127
5	0.060	1ihgA	0.750	2.18	0.137	0.841	5.2.1.8	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	0.06	3kd7B	0.574	1.35	0.180	0.614	1.00	III	complex1.pdb.gz	25,29,32,33,62,65,66,69,73
2	0.05	2xcbA	0.667	1.79	0.122	0.736	0.80	III	complex2.pdb.gz	62,65,66,69,72,114,117
3	0.04	2fi70	0.753	2.07	0.159	0.859	1.18	III	complex3.pdb.gz	81,82,86,88,89,112,127,130,131,134
4	0.03	1hz40	0.713	3.21	0.140	0.920	0.80	III	complex4.pdb.gz	34,35,40,66,69,73
5	0.03	3fp4A	0.738	2.52	0.116	0.896	0.65	III	complex5.pdb.gz	113,117,120,132,144

	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.