D-I-TASSER Q3SXZ7-D1

D-I-TASSER results for Q3SXZ7-D1

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

Input Sequence in FASTA format

>Q3SXZ7 (102 residues)
MVPSREALLGPGTTAIRCPKKLQNQNYKGHGLSKGKEREQRASIRFKTTLMNTLMDVLRH
RPGWVEVKDEGEWDFYWCDVSWLRENFDHTYMDEHVRISHFR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MVPSREALLGPGTTAIRCPKKLQNQNYKGHGLSKGKEREQRASIRFKTTLMNTLMDVLRHRPGWVEVKDEGEWDFYWCDVSWLRENFDHTYMDEHVRISHFR
Prediction	CCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCHHHHHHHCCCCSSCCCCCCSSSSSCCHHHHHHHCCCCCCCCCSSCCCCC
Confidence	987643110489886546543221357655676410136788637896488609999861679675278997479962568999861445488771505669
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MVPSREALLGPGTTAIRCPKKLQNQNYKGHGLSKGKEREQRASIRFKTTLMNTLMDVLRHRPGWVEVKDEGEWDFYWCDVSWLRENFDHTYMDEHVRISHFR
Prediction	744555424247555454253155543544445545646754303020416411241046353144157654010100334203420453405741413238
	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 AttentionPotential. 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

CCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCHHHHHHHCCCCSSCCCCCCSSSSSCCHHHHHHHCCCCCCCCCSSCCCCC
MVPSREALLGPGTTAIRCPKKLQNQNYKGHGLSKGKEREQRASIRFKTTLMNTLMDVLRHRPGWVEVKDEGEWDFYWCDVSWLRENFDHTYMDEHVRISHFR

6vzqA

0.23

0.14

4.30

1.04

SPARKS-K

--------------------------------------KKRLVINLSNCRYDSVRRAAQQYG-LREAGDNDDWTLYWTDYSVSLERVME--MKSYQKINHFP

4ylrA

0.21

0.12

3.74

1.19

CNFpred

------------------------------------------TANVAGTKFEIVRLVIDE-MGFMKTPDDETSNLIWCDSAVQQEKIS--ELQNYQRINHFP

6vzqA2

0.22

0.13

4.02

2.35

HHsearch

----------------------------------------KKRLVINLSNYDSVRRAAQQ-YGLREAGDNDDWTLYWTDYSVSLERV--MEMKSYQKINHFP

4eb0A

0.05

2.32

0.66

CEthreader

TRSALTADGPFSVATYTVSRLSVSGFGGGVIYYPTGTSLTFGGIAMSPGLAWLGRRLASHGFVVLVINTNSRAVAGHSMGGGGTLRIAEQNPSLKAAVPLTP

2r79A2

0.07

2.84

0.60

EigenThreader

DLEALESNLKKLGDWLGVLDYRQRLRRQADWIAAAQKSQPAPGVLLVAGRNTGGDWVLNRA-GARNLATHEGAVVIADRRAALLKQNPGLAARDGRLLVLDP

7jfrF

0.10

0.06

2.18

0.58

FFAS-3D

------------------------------------------MYTFVVRDENEVSRLLLATGQWKRLRKDPRFNLMLGERNRLPFGRLGHEPGLVQLVNYYR

6vzqA2

0.23

0.14

4.30

1.01

SPARKS-K

--------------------------------------KKRLVINLSNCRYDSVRRAAQQYG-LREAGDNDDWTLYWTDYSVSLERVME--MKSYQKINHFP

6vzwA

0.24

0.13

3.98

1.12

CNFpred

-------------------------------------------LVINLS-YDSVRRAAQQ-YGLREAGDNDDWTLYWTDYSVSLERVM--EMKSYQKINHFP

4gvlA2

0.06

0.05

2.20

1.00

DEthreader

---RYIRAT---TC-GALAHI----QTKSQLAALEYLIGEAPEELIFIIGHCAAAAFLDRKP-VPFIAGIDRAGIIVTTDSTNIF-LTLACRHSIRIVARVS

3b7wA

0.04

2.02

0.68

MapAlign

-PSPALWWVNGKGKELMWNFRELSENSQQAANVLSGACGLQRGDRVAVVLWWLVILGCIR-AGLIFMLQMSKAKAIVAGIQEVDTVA--SECPSLRIKLLVS

(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	0.5456

(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 AttentionPotential, 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	4gvlA2	0.52	4.31	0.090	0.902	model1_4gvlA2.pdb.gz
2	5kf6A	0.52	3.77	0.044	0.853	model1_5kf6A.pdb.gz
3	1kzyC	0.52	3.46	0.099	0.784	model1_1kzyC.pdb.gz
4	3k0kA	0.51	4.05	0.089	0.853	model1_3k0kA.pdb.gz
5	2adoB	0.51	3.47	0.052	0.774	model1_2adoB.pdb.gz
6	2nteA	0.49	3.74	0.052	0.784	model1_2nteA.pdb.gz
7	2vxcB	0.47	3.83	0.056	0.765	model1_2vxcB.pdb.gz
8	3se7A	0.47	4.05	0.071	0.853	model1_3se7A.pdb.gz
9	1l0bA	0.43	3.72	0.060	0.676	model1_1l0bA.pdb.gz
10	3wqoA	0.40	4.32	0.048	0.755	model1_3wqoA.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	0.80	catalytic activity
GO:0016874	0.73	ligase activity
GO:0070739	0.71	protein-glutamic acid ligase 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	0.94	cellular process
GO:0008152	0.90	metabolic process
GO:0071704	0.89	organic substance metabolic process
GO:0044238	0.89	primary metabolic process
GO:0044237	0.89	cellular metabolic process
GO:0044260	0.88	cellular macromolecule metabolic process
GO:0006464	0.85	cellular protein modification process
GO:0018095	0.83	protein polyglutamylation
GO:0044699	0.65	single-organism process
GO:0044763	0.58	single-organism cellular process
GO:0016043	0.51	cellular component organization

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	0.99	cell part
GO:0044424	0.95	intracellular part
GO:0044446	0.87	intracellular organelle part
GO:0044430	0.85	cytoskeletal part
GO:0044441	0.84	ciliary part
GO:0036064	0.83	ciliary basal body
GO:0016020	0.83	membrane
GO:0005886	0.64	plasma membrane
GO:0043226	0.57	organelle
GO:0044425	0.50	membrane 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	2q8nB	0.475	4.47	0.059	0.863	5.3.1.9	NA
2	0.060	1w30B	0.485	3.42	0.058	0.735	2.4.2.9	NA
3	0.060	1pg3B	0.465	4.15	0.055	0.765	6.2.1.1	63,70
4	0.060	2qedA	0.470	3.90	0.071	0.804	3.1.2.6	NA
5	0.060	2bkvB	0.474	4.45	0.046	0.853	3.5.99.6	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	0.01	3k16A	0.505	4.03	0.100	0.853	0.23	III	complex1.pdb.gz	48,53,55,74
2	0.01	3k0hA	0.508	4.06	0.091	0.853	0.15	III	complex2.pdb.gz	59,60,62
3	0.01	3cojB	0.463	4.05	0.082	0.794	0.15	III	complex3.pdb.gz	9,73,74
4	0.01	1t2vD	0.505	3.93	0.094	0.824	0.14	III	complex4.pdb.gz	12,55,56,57
5	0.01	3k0kA	0.512	4.05	0.089	0.853	0.15	III	complex5.pdb.gz	46,47,72
6	0.01	1kzy2	0.518	3.46	0.099	0.784	0.12	III	complex6.pdb.gz	42,43,45
7	0.01	3cojA	0.501	4.12	0.069	0.853	0.11	III	complex7.pdb.gz	10,51,52
8	0.01	1t29A	0.509	3.98	0.101	0.843	0.10	III	complex8.pdb.gz	7,8,10,63,64
9	0.01	3cojF	0.500	3.82	0.082	0.824	0.10	III	complex9.pdb.gz	44,45,47

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.