D-I-TASSER Q00889-D3

D-I-TASSER results for Q00889-D3

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

Input Sequence in FASTA format

>Q00889 (91 residues)
LPMPYITINNLNPREKKDVLAFTCEPKSRNYTYIWWLNGQSLPVSPRVKRPIENRILILP
SVTRNETGPYQCEIRDRYGGIRSNPVTLNVL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| LPMPYITINNLNPREKKDVLAFTCEPKSRNYTYIWWLNGQSLPVSPRVKRPIENRILILPSVTRNETGPYQCEIRDRYGGIRSNPVTLNVL
Prediction	CCCCSSSCCCCSSSSCCCCSSSSSSCCCCCCSSSSSSCCSSCCCCCCSSSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCCSSSSSSSSSSC
Confidence	9998898489626737831999999399996189999999947888589927998899956684557799999994886358610999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| LPMPYITINNLNPREKKDVLAFTCEPKSRNYTYIWWLNGQSLPVSPRVKRPIENRILILPSVTRNETGPYQCEIRDRYGGIRSNPVTLNVL
Prediction	7542504345443446443030344176451312123445504645424136743303046045624140334041543454144140426
	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

                   |                   |                   |                   |

SS
Seq

CCCCSSSCCCCSSSSCCCCSSSSSSCCCCCCSSSSSSCCSSCCCCCCSSSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCCSSSSSSSSSSC
LPMPYITINNLNPREKKDVLAFTCEPKSRNYTYIWWLNGQSLPVSPRVKRPIENRILILPSVTRNETGPYQCEIRDRYGGIRSNPVTLNVL

1l6zA2

0.28

0.27

8.41

1.50

DEthreader

VTQPFLQVTNT-TVKELDSVTLTCLSNDIGANIQWLFNSQSLQLTERMTLSQNNSILRIDPIKREDAGEYQCEISNPVSVRRSNSIKLDII

7ahsA3

0.15

5.15

1.10

SPARKS-K

AEPIQFTKRQNIVVSEHQSATFECEVSFDDAIVTWYKGPTELTESQKYNFRNDGHYMTIHNVTPDDEGVYSVIARLEPRGEARSTAELYLT

6ul6B

0.12

4.23

0.45

MapAlign

-LQLVESG--GGLVQPGGSLRLSCVVSGNTYIMGWYRQVELVSVKGRFTISKNTVYLQMFGLKPEDAGNYVCNADWYGIDYWGKGTLVTVS

1l6zA2

0.28

0.27

8.41

0.39

CEthreader

VTQPFLQVTNT-TVKELDSVTLTCLSNDIGANIQWLFNSQSLQLTERMTLSQNNSILRIDPIKREDAGEYQCEISNPVSVRRSNSIKLDII

1e07A7

0.53

15.24

1.20

MUSTER

LPKPSISSNNSKPVEDKDAVAFTCEPETQDATYLWWVNNQSLPVSPRLQLSNGNRTLTLFNVTRNDTASYKCETQNPVSARRSDSVILNVL

6grqA

0.22

6.93

0.40

HHsearch

LPKPILRVQPDSVVSRWTKVTFFCEETIGANEYRLYKDGKLYKTVTKNKKPANKAEFSLSNVDLSNAGQYECSYSTQYKSSYSDPLKLVVT

1e07A4

0.54

15.53

1.62

FFAS-3D

LPKPSISSNNSKPVEDKDAVAFTCEPEAQNTTYLWWVNGQSLPVSPRLQLSNGNRTLTLFNVTRNDARAYVCGIQNSVSANRSDPVTLDV-

2dm2A

0.17

0.16

5.43

0.28

EigenThreader

APFFEMKL-KHYKIFEGMPVTFTCRVAGNPPKIYWFKDGKQISPSDHYTIQRLDGTLHTTASTLDDDGNYTIMAANPQGRISC-TGRLMVQ

5f1dA

0.27

0.26

8.11

1.62

CNFpred

VTQPSLQVT-NTTVKELDSVTLTCLSNDIGANIQWLFNSQSLQLTERMTLSQNNSILRIDPIKREDAGEYQCEISNPVSVKRSNSIKLDII

1l6zA

0.28

0.27

8.41

1.50

DEthreader

VTQPFLQVTNT-TVKELDSVTLTCLSNDIGANIQWLFNSQSLQLTERMTLSQNNSILRIDPIKREDAGEYQCEISNPVSVRRSNSIKLDII

(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	0.8944

(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	1l6zA2	0.93	1.02	0.278	0.989	model1_1l6zA2.pdb.gz
2	6cvkB	0.86	1.73	0.144	0.989	model1_6cvkB.pdb.gz
3	3nl4L1	0.86	1.76	0.111	0.989	model1_3nl4L1.pdb.gz
4	5lx9H2	0.86	1.79	0.133	0.989	model1_5lx9H2.pdb.gz
5	6pscA	0.86	1.77	0.111	0.989	model1_6pscA.pdb.gz
6	3kg5A	0.86	1.69	0.135	0.978	model1_3kg5A.pdb.gz
7	6ye3B1	0.86	1.81	0.111	0.989	model1_6ye3B1.pdb.gz
8	6cr1L	0.85	1.87	0.122	0.989	model1_6cr1L.pdb.gz
9	6xqqB1	0.85	1.75	0.100	0.989	model1_6xqqB1.pdb.gz
10	4hjjL2	0.85	1.85	0.089	0.989	model1_4hjjL2.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:0042802	0.57	identical protein 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:0065007	0.81	biological regulation
GO:0050789	0.77	regulation of biological process
GO:0032501	0.77	multicellular organismal process
GO:0050794	0.74	regulation of cellular process
GO:0051704	0.63	multi-organism process
GO:0007565	0.60	female pregnancy

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	0.93	cell part
GO:0044421	0.71	extracellular region part
GO:0043226	0.61	organelle
GO:0016020	0.61	membrane
GO:0044425	0.59	membrane part
GO:0043227	0.59	membrane-bounded organelle
GO:0031224	0.53	intrinsic component of membrane
GO:0005886	0.53	plasma membrane
GO:0044459	0.52	plasma membrane part
GO:0016021	0.50	integral component of 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	0.228	2wwmD	0.800	2.06	0.159	0.967	2.7.11.1	39
2	0.209	2eo1A	0.752	2.24	0.214	0.923	2.7.11.1	42,73
3	0.172	2edrA	0.700	2.28	0.169	0.912	2.7.11.1	24,47,82
4	0.167	1u2hA	0.816	1.84	0.159	0.967	2.7.11.1	38
5	0.148	2edwA	0.735	2.03	0.169	0.912	2.7.11.1	24,42

	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	0.18	3leyL	0.849	1.86	0.133	0.989	0.68	III	complex1.pdb.gz	40,75,76,78,80
2	0.18	3qg6L	0.834	1.97	0.167	0.989	0.66	III	complex2.pdb.gz	33,35,40,80
3	0.16	1mj7L	0.826	2.04	0.156	0.989	0.62	HAL	complex3.pdb.gz	33,37,72,74,75,81
4	0.15	1wc7A	0.838	1.88	0.122	0.989	0.71	PP3	complex4.pdb.gz	32,33,35,75,76,79,81
5	0.06	1indH	0.814	2.08	0.149	0.956	0.75	EOT	complex5.pdb.gz	40,42,70,71
6	0.04	1nd0A	0.842	1.90	0.144	0.989	0.62	DP4	complex6.pdb.gz	38,69,70,86
7	0.04	1kn4L	0.854	1.82	0.133	0.989	0.67	PDE	complex7.pdb.gz	36,38,69,71,86,88
8	0.04	2w65D	0.837	1.95	0.133	0.989	0.63	III	complex8.pdb.gz	39,68,88

	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.