D-I-TASSER Q9Y5M8-D1

D-I-TASSER results for Q9Y5M8-D1

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

Input Sequence in FASTA format

>Q9Y5M8 (271 residues)
MASADSRRVADGGGAGGTFQPYLDTLRQELQQTDPTLLSVVVAVLAVLLTLVFWKLIRSR
RSSQRAVLLVGLCDSGKTLLFVRLLTGLYRDTQTSITDSCAVYRVNNNRGNSLTLIDLPG
HESLRLQFLERFKSSARAIVFVVDSAAFQREVKDVAEFLYQVLIDSMGLKNTPSFLIACN
KQDIAMAKSAKLIQQQLEKELNTLRVTRSAAPSTLDSSSTAPAQLGKKGKEFEFSQLPLK
VEFLECSAKGGRGDVGSADIQDLEKWLAKIA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MASADSRRVADGGGAGGTFQPYLDTLRQELQQTDPTLLSVVVAVLAVLLTLVFWKLIRSRRSSQRAVLLVGLCDSGKTLLFVRLLTGLYRDTQTSITDSCAVYRVNNNRGNSLTLIDLPGHESLRLQFLERFKSSARAIVFVVDSAAFQREVKDVAEFLYQVLIDSMGLKNTPSFLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTRSAAPSTLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDVGSADIQDLEKWLAKIA
Prediction	CCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCCCCHHHHHHHHHCCCCCCSSCCCCCCSSSSSSSCCCCCSSSSSSCCCCHHHHHHHHHHHHHHCCSSSSSSSCCCCCCHHHHHHHHHHHHHHCHHHHCCCCSSSSSSSCCCCCCCCCHHHHHHHHHHHHHHCCCSSSSCCSCCCCCCCCCCCCCCCCCCSSSCCCCCSSSSSSSSSSCCCCCCCCCCHHHHHHHHHHHC
Confidence	9864210011125778765026999999986179729999999999999999999974256787589998789987799999981699764453566857899996379958999988998379999999998509889999969986312999999999997393664379809999756467689999999999986655312216621020357766543256778544642379738999988524787522124189999999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MASADSRRVADGGGAGGTFQPYLDTLRQELQQTDPTLLSVVVAVLAVLLTLVFWKLIRSRRSSQRAVLLVGLCDSGKTLLFVRLLTGLYRDTQTSITDSCAVYRVNNNRGNSLTLIDLPGHESLRLQFLERFKSSARAIVFVVDSAAFQREVKDVAEFLYQVLIDSMGLKNTPSFLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTRSAAPSTLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDVGSADIQDLEKWLAKIA
Prediction	7433434331544346450341054035305644111000211331332332323203444644110000003504000001103576346231133242331314334513010000021440043005301640300000000023653153015203500444623752000000022031560242730262054203523413133032232444434313554350305507140200001044464654554054035005637
	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                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCCCCHHHHHHHHHCCCCCCSSCCCCCCSSSSSSSCCCCCSSSSSSCCCCHHHHHHHHHHHHHHCCSSSSSSSCCCCCCHHHHHHHHHHHHHHCHHHHCCCCSSSSSSSCCCCCCCCCHHHHHHHHHHHHHHCCCSSSSCCSCCCCCCCCCCCCCCCCCCSSSCCCCCSSSSSSSSSSCCCCCCCCCCHHHHHHHHHHHC
MASADSRRVADGGGAGGTFQPYLDTLRQELQQTDPTLLSVVVAVLAVLLTLVFWKLIRSRRSSQRAVLLVGLCDSGKTLLFVRLLTGLYRDTQTSITDSCAVYRVNNNRGNSLTLIDLPGHESLRLQFLERFKSSARAIVFVVDSAAFQREVKDVAEFLYQVLIDSMGLKNTPSFLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTRSAAPSTLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDVGSADIQDLEKWLAKIA

2fh5B

0.87

0.59

16.73

1.00

DEthreader

----------------------------------------------------------------RAVLFVGLCDSGKTLLFVRLLTGQYRDTQTSITDSSAIYKVNNNRGNSLTLIDLPGHESLRFQLLDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAKSAKLIQQQLEKELNTLR-VTR-------------PAQLGKKGKFEFSQLPLKVEFLECSAKS------A-DIQDLEKWLAKIA

2fh5B

0.93

0.65

18.13

1.46

SPARKS-K

----------------------------------------------------------------RAVLFVGLCDSGKTLLFVRLLTGQYRDTQTSITDSSAIYKVNNNRGNSLTLIDLPGHESLRFQLLDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTRS------------PAQLGKKGKEFEFSQLPLKVEFLECSA-------KSADIQDLEKWLAKIA

5ck3B

0.29

0.20

6.19

0.55

MapAlign

----------------------------------------------------------------PSVLLIGPSGAGKTALLTLFETSPVAQTHTSQVPTSVELAVGAATARKFLLIDTPGHPKLRGTTLQHLLLTLKAVIFLLDAAALADYLSQTASYLYDVLLSLQKRPSSIPVLIAANKQDLFTAVPASLVKSRLEHELGRIR----------KTRQKGGWLGAVGSKEFEMMEFDMEVEVMGGNVIG-----DGPGAERWWRWIGERI

2fh5B

0.93

0.64

18.03

0.41

CEthreader

----------------------------------------------------------------RAVLFVGLCDSGKTLLFVRLLTGQYRDTQTSITDSSAIYKVNNNRGNSLTLIDLPGHESLRFQLLDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTRSPA------------QLGKKGKEFEFSQLPLKVEFLECSAKS-------ADIQDLEKWLAKIA

2fh5B

0.93

0.64

18.03

1.22

MUSTER

----------------------------------------------------------------RAVLFVGLCDSGKTLLFVRLLTGQYRDTQTSITDSSAIYKVNNNRGNSLTLIDLPGHESLRFQLLDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTR------------SPAQLGKKGKEFEFSQLPLKVEFLECSAKS-------ADIQDLEKWLAKIA

2fh5B

0.93

0.64

18.03

0.91

HHsearch

----------------------------------------------------------------RAVLFVGLCDSGKTLLFVRLLTGQYRDTQTSITDSSAIYKVNNNRGNSLTLIDLPGHESLRFQLLDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTRS------------PAQLGKKGKEFEFSQLPLKVEFLECSAKS-A------DIQDLEKWLAKIA

2fh5B

0.92

0.64

17.93

2.03

FFAS-3D

----------------------------------------------------------------RAVLFVGLCDSGKTLLFVRLLTGQYRDTQTSITDSSAIYKVNNNRGNSLTLIDLPGHESLRFQLLDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTR------------SPAQLGKKGKEFEFSQLPLKVEFLECSAKSA-------DIQDLEKWLAKIA

3lvqE

0.15

0.12

4.11

0.70

EigenThreader

GQDFGQPLPGPDAQAPEELVLHLAVKVHYAALYNQPDCLKLLLKGIARKKECEELLEQAQANKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTY--KNVKFNVWDVGGQDK--IRPLWRHYYTGTQGLIFVVDC-ADRDRIDEARQELHRIIND--REMRDAIILIFANKQDLPDAMKPHEIQEKL----------------------------GLTRIR------DRNWYVQPSCA------TSGDGLYEGLTWLTSNY

2fh5B

0.94

0.65

18.23

1.50

CNFpred

----------------------------------------------------------------RAVLFVGLCDSGKTLLFVRLLTGQYRDTQTSITDSSAIYKVNNNRGNSLTLIDLPGHESLRFQLLDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTRS------------PAQLGKKGKEFEFSQLPLKVEFLECSAK-------SADIQDLEKWLAKIA

5ck3B

0.30

0.21

6.38

1.00

DEthreader

----------------------------------------------------------------PSVLLIGPSGAGKTALLTLFERGPVAQTHTSQVPTSVELAVGANTARKFLLIDTPGHPKLRGTTLQHLLLTLKAVIFLLDAAALAGYLSQTASYLYDVLLSLKRSRSSIPVLIAANKQDLFTAVPASLVKSRLEHELGRIRKTRQK-G---------W-LGAVGSKEFKFEEMMMEVEVMGGNVI--GD-G--PGAERWWRWIGERI

(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	0.6452

(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	2fh5B	0.68	0.87	0.904	0.694	model1_2fh5B.pdb.gz
2	5ck3B	0.67	1.58	0.302	0.709	model1_5ck3B.pdb.gz
3	6bbpA	0.65	3.26	0.170	0.749	model1_6bbpA.pdb.gz
4	1nrjB	0.63	2.04	0.286	0.683	model1_1nrjB.pdb.gz
5	1f5nA1	0.60	4.12	0.105	0.786	model1_1f5nA1.pdb.gz
6	2qtvB	0.55	2.08	0.222	0.594	model1_2qtvB.pdb.gz
7	4dheA	0.53	3.36	0.149	0.638	model1_4dheA.pdb.gz
8	2gf0B	0.53	2.90	0.177	0.605	model1_2gf0B.pdb.gz
9	1f6bB	0.52	2.68	0.179	0.583	model1_1f6bB.pdb.gz
10	1fzqA	0.51	2.43	0.197	0.565	model1_1fzqA.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:0005047	0.86	signal recognition particle binding
GO:1901363	0.56	heterocyclic compound binding
GO:0097159	0.56	organic cyclic compound 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:0009987	0.99	cellular process
GO:0044763	0.95	single-organism cellular process
GO:0051179	0.94	localization
GO:0016043	0.94	cellular component organization
GO:0006810	0.92	transport
GO:1902578	0.91	single-organism localization
GO:0071702	0.90	organic substance transport
GO:0046907	0.89	intracellular transport
GO:0044765	0.89	single-organism transport
GO:0015031	0.89	protein transport
GO:0090150	0.88	establishment of protein localization to membrane
GO:0072657	0.88	protein localization to membrane
GO:0006605	0.88	protein targeting
GO:0045047	0.87	protein targeting to ER
GO:0006613	0.87	cotranslational protein targeting to membrane
GO:0006614	0.86	SRP-dependent cotranslational protein targeting to membrane
GO:0008152	0.64	metabolic process
GO:0044237	0.57	cellular 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:0044424	1.00	intracellular part
GO:0044444	0.98	cytoplasmic part
GO:0044446	0.97	intracellular organelle part
GO:0044425	0.87	membrane part
GO:0032991	0.85	macromolecular complex
GO:0044432	0.83	endoplasmic reticulum part
GO:0098796	0.82	membrane protein complex
GO:0005785	0.81	signal recognition particle receptor complex

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	0.491	1m2oB	0.552	2.10	0.222	0.594	3.6.5.-	121
2	0.138	2bmeA	0.540	2.33	0.183	0.598	3.6.5.2	NA
3	0.122	2f9mA	0.533	2.44	0.174	0.594	3.6.5.2	NA
4	0.120	1d2eA	0.517	3.25	0.142	0.624	3.6.5.3	74,121
5	0.085	1aa9A	0.507	2.86	0.174	0.594	3.6.5.-	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	0.96	2fh5B	0.681	0.87	0.904	0.694	1.83	GTP	complex1.pdb.gz	73,74,75,76,77,78,79,92,94,95,120,180,181,183,184,247,248,249
	2	0.15	3ab3A	0.536	2.59	0.139	0.609	0.85	ALF	complex2.pdb.gz	73,74,77,118,119,120,121

	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.