D-I-TASSER P47897-D3

D-I-TASSER results for P47897-D3

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

Input Sequence in FASTA format

>P47897 (113 residues)
VLESLRVIITNFPAAKSLDIQVPNFPADETKGFHQVPFAPIVFIERTDFKEEPEPGFKRL
AWGQPVGLRHTGYVIELQHVVKGPSGCVESLEVTCRRADAGEKPKAFIHWVSQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| VLESLRVIITNFPAAKSLDIQVPNFPADETKGFHQVPFAPIVFIERTDFKEEPEPGFKRLAWGQPVGLRHTGYVIELQHVVKGPSGCVESLEVTCRRADAGEKPKAFIHWVSQ
Prediction	CCCCSSSSSSSCCCCCSSSSSSCCCCCCCCCCSSSSSSCCSSSSSHHHCCCCCCCCCSSCCCCCSSSSCCCCSSSSSSSSSSCCCCCSSSSSSSSCCCCCCCCCCSSSSCCCC
Confidence	98738999964899938999946999994335268643665999724411479878533289967886133337999999988999889999998788779866649980329
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| VLESLRVIITNFPAAKSLDIQVPNFPADETKGFHQVPFAPIVFIERTDFKEEPEPGFKRLAWGQPVGLRHTGYVIELQHVVKGPSGCVESLEVTCRRADAGEKPKAFIHWVSQ
Prediction	73421302021145743240303312734733425140344010435304453575032024644020331322030451443773513203031556875430303135248
	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

CCCCSSSSSSSCCCCCSSSSSSCCCCCCCCCCSSSSSSCCSSSSSHHHCCCCCCCCCSSCCCCCSSSSCCCCSSSSSSSSSSCCCCCSSSSSSSSCCCCCCCCCCSSSSCCCC
VLESLRVIITNFPAAKSLDIQVPNFPADETKGFHQVPFAPIVFIERTDFKEEPEPGFKRLAWGQPVGLRHTGYVIELQHVVKGPSGCVESLEVTCRRADAGEKPKAFIHWVSQ

5bnzA2

0.35

0.34

10.05

1.33

DEthreader

LK-PLKVVITNYPEGQVENLELPRHP-KEDMGVRVLPFGRELFIDAGDFEEVPPAGYKRLIPGGEVRLRG-SYVIRADEAIKDADGNIVELRCSYDDTLKNPKVKGVIHWVPA

5zdkA3

0.44

0.42

12.19

2.45

SPARKS-K

-VDPLKVVLTNYEG--EEWIEAPYWPRIPKEGTRPLPFSPELYIERTDFSLNPPKGWKRLAPGQRVRLRHA-YVIELEDVVEE-GGEVRLLKARIVPGEDGVRPKGVIHWVSA

2hz7A2

0.31

0.29

8.84

1.32

MapAlign

VLDPVKVTLTNLDG--EKTLSLPYMRVAPEEAVRDVPLTRELYIERDDFSPAPPKGFKRLTPGGTVRLRGA-GIIRADDFGTDEAGQVTHIRATLL--GEDAKAAGVIHWVSA

2hz7A2

0.33

0.32

9.56

1.23

CEthreader

VLDPVKVTLTNLDG--EKTLSLPYWPHDVVRAVRDVPLTRELYIERDDFSPAPPKGFKRLTPGGTVRLRGA-GIIRADDFGTDEAGQVTHIRATLLGED--AKAAGVIHWVSA

5zdkA3

0.44

0.42

12.42

2.19

MUSTER

-VDPLKVVLTNYEGE--EWIEAPYWPRDPKEGTRPLPFSPELYIERTDFSLNPPKGWKRLAPGQRVRLRHA-YVIELEDVVEE-GGEVRLLKARIVPGEDGVRPKGVIHWVSA

4h3sA2

0.30

0.29

8.86

3.20

HHsearch

VLDPVEVVVDNLSDDYEELATIPYRPGTPEFGERTVPFTNKFYIERSDFSENDDKEFFRLTPNQPVGLIKVSHTVSFKSLEKDEAGKIIRIHVNYDNK---KKPKTYIQWVPI

5zdkA3

0.43

0.41

11.95

1.71

FFAS-3D

-VDPLKVVLTNYEGE--EWIEAPYWPRDPKEGTRPLPFSPELYIERTDFSLNPPKGWKRLAPGQRVRLRHAYV-IELEDVVEE-GGEVRLLKARIVPGEDGVRPKGVIHWVSA

5zdkA3

0.41

0.39

11.47

1.35

EigenThreader

-VDPLKVVLTNYEG--EEWIEAPWPRDIPKEGTRPLPFSPELYIERTDFSLNPPKGWKRLAPGQRVRLRHA-YVIELEDVVEEG-GEVRLLKARIVPGTDGVRPKGVIHWARH

4h3sA

0.30

0.29

8.86

2.05

CNFpred

VLDPVEVVVDNLSDDYEELATIPYRPGTPEFGERTVPFTNKFYIERSDFSENDDKEFFRLTPNQPVGLIKVSHTVSFKSLEKDEAGKIIRIHVNYDNK---KKPKTYIQWVPI

5bnzA

0.35

0.34

10.05

1.33

DEthreader

LK-PLKVVITNYPEGQVENLELPRHP-KEDMGVRVLPFGRELFIDAGDFEEVPPAGYKRLIPGGEVRLRG-SYVIRADEAIKDADGNIVELRCSYDDTLKNPKVKGVIHWVPA

(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	0.8441

(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	5bnzA	0.92	1.08	0.369	0.982	model1_5bnzA.pdb.gz
2	5zdkA	0.90	1.15	0.440	0.965	model1_5zdkA.pdb.gz
3	2hz7A	0.90	1.16	0.324	0.956	model1_2hz7A.pdb.gz
4	4h3sA2	0.88	1.52	0.303	0.965	model1_4h3sA2.pdb.gz
5	1qrtA	0.86	1.30	0.340	0.929	model1_1qrtA.pdb.gz
6	4p2bA	0.82	1.24	0.380	0.885	model1_4p2bA.pdb.gz
7	1w98B	0.33	4.16	0.068	0.575	model1_1w98B.pdb.gz
8	3tsaA	0.31	4.63	0.071	0.566	model1_3tsaA.pdb.gz
9	2cfoB	0.31	4.90	0.041	0.584	model1_2cfoB.pdb.gz
10	1g59A1	0.31	4.56	0.027	0.557	model1_1g59A1.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:1901363	1.00	heterocyclic compound binding
GO:0097159	1.00	organic cyclic compound binding
GO:0004819	1.00	glutamine-tRNA ligase activity
GO:0003723	0.99	RNA 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	0.93	cellular process
GO:0008152	0.91	metabolic process
GO:0071704	0.90	organic substance metabolic process
GO:0044238	0.89	primary metabolic process
GO:0044237	0.89	cellular metabolic process
GO:0043170	0.87	macromolecule metabolic process
GO:0034641	0.87	cellular nitrogen compound metabolic process
GO:0044699	0.86	single-organism process
GO:0044260	0.86	cellular macromolecule metabolic process
GO:1901564	0.84	organonitrogen compound metabolic process
GO:0044763	0.84	single-organism cellular process
GO:0044710	0.84	single-organism metabolic process
GO:0006139	0.84	nucleobase-containing compound metabolic process
GO:0090304	0.83	nucleic acid metabolic process
GO:0044281	0.83	small molecule metabolic process
GO:0016070	0.82	RNA metabolic process
GO:0034660	0.81	ncRNA metabolic process
GO:0019752	0.81	carboxylic acid metabolic process
GO:0006418	0.80	tRNA aminoacylation for protein translation
GO:0006425	0.78	glutaminyl-tRNA aminoacylation

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	0.90	cytoplasmic part
GO:0005829	0.81	cytosol
GO:0043226	0.79	organelle
GO:0043229	0.78	intracellular organelle
GO:0043227	0.76	membrane-bounded organelle
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0005739	0.71	mitochondrion

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	1cb5A	0.423	4.52	0.047	0.761	3.4.22.40	NA
2	0.060	2hd5A	0.326	4.77	0.076	0.620	3.1.2.15	NA
3	0.060	1sy7A	0.412	4.70	0.077	0.770	1.11.1.6	NA
4	0.060	3eqvA	0.434	4.79	0.073	0.814	3.4.16.4	74,94
5	0.060	1skfA	0.413	4.70	0.066	0.761	3.4.16.4	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	0.12	1o0cA	0.851	1.32	0.340	0.929	0.23	AMP	complex1.pdb.gz	42,44,45,68
2	0.10	1o0bA	0.857	1.27	0.340	0.929	0.24	AMP	complex2.pdb.gz	38,67,68,71
3	0.07	1o0bA	0.857	1.27	0.340	0.929	0.23	GLN	complex3.pdb.gz	48,50,62
4	0.07	2rd2A	0.858	1.25	0.340	0.929	0.17	QSI	complex4.pdb.gz	45,47,48,50,105
5	0.06	2re8A	0.859	1.24	0.340	0.929	0.13	GSU	complex5.pdb.gz	35,36,37,38,39
6	0.01	2c8cB	0.449	4.66	0.045	0.761	0.11	NAD	complex6.pdb.gz	46,48,67
7	0.01	2xfsA	0.438	4.32	0.039	0.752	0.28	J01	complex7.pdb.gz	68,73,75
8	0.01	1yhu5	0.334	4.70	0.099	0.628	0.12	III	complex8.pdb.gz	46,57,58,59
9	0.01	2c8fE	0.298	5.35	0.039	0.620	0.13	NAD	complex9.pdb.gz	43,44,45,47,48,63
10	0.01	3humB	0.447	4.73	0.055	0.832	0.20	CEW	complex10.pdb.gz	67,68,74

	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.