D-I-TASSER P62701-D1

D-I-TASSER results for P62701-D1

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

Input Sequence in FASTA format

>P62701 (114 residues)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRI

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRI
Prediction	CCCCCCCHHHHHCCCCCCCSCCCCCSSSSCCCCCCCCCCCCCCHHHHHHHHHCHCCCHHHHHHHHHCCCSSSCCSSSCCCCCCCCCSSSSSSCCCCCSSSSSSCCCCCSSSSSC
Confidence	998752111210387424405556747416999998742241239999988612255999999988490898785763465677511699973679759999769974898849
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRI
Prediction	876454422322412541415446432133334342534401000000343042033352024014552021414224444212212210304646520100116533023366
	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

CCCCCCCHHHHHCCCCCCCSCCCCCSSSSCCCCCCCCCCCCCCHHHHHHHHHCHCCCHHHHHHHHHCCCSSSCCSSSCCCCCCCCCSSSSSSCCCCCSSSSSSCCCCCSSSSSC
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRI

5xyiE

0.61

0.59

16.83

1.33

DEthreader

--C-QRFHLKRLTAPHHWLL-AKSGKFASHPSTGPHKLRECLPINIFLRDRLKYALTAKEAVAIVKRRLVKVDGKVRTNYRYPTGLMDVIGLGKSNELFRIIYDCKGRFCVHHI

3j38E2

0.81

22.79

4.68

SPARKS-K

MARGPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYPAGYMDVITLEKTGEFFRLVYDVKGRFVIHRI

3j7aF

0.65

0.61

17.52

1.21

MapAlign

-------HLKRVNAPSHWMLNKMGGQYAPKTSSGPHKLLESIPLVILLRNRLKYALTFDEVKMILIQKIVKVDNKVRTDCTFPVGLMDVIHITKSNEYFRLLYDIKGRFVPHRI

3j7aF

0.65

0.64

18.28

0.92

CEthreader

-GKGIKKHLKRVNAPSHWMLNKMGGQYAPKTSSGPHKLLESIPLVILLRNRLKYALTFDEVKMILIQKIVKVDNKVRTDCTFPVGLMDVIHITKSNEYFRLLYDIKGRFVPHRI

3j38E2

0.81

22.79

3.61

MUSTER

MARGPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYPAGYMDVITLEKTGEFFRLVYDVKGRFVIHRI

3j38E

0.81

22.79

2.65

HHsearch

MARGPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYPAGYMDVITLEKTGEFFRLVYDVKGRFVIHRI

3j38E2

0.81

22.79

2.20

FFAS-3D

MARGPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYPAGYMDVITLEKTGEFFRLVYDVKGRFVIHRI

3j38E

0.81

22.79

1.35

EigenThreader

MARGPKKHLKRLAAPKAWMLDKLGGVFAPRPSTGPHKLRESLPLLIFLRNRLKYALNGAEVTKIVMQRLVKVDGKVRTDPTYPAGYMDVITLEKTGEFFRLVYDVKGRFVIHRI

4cxcE

0.95

0.94

26.33

2.56

CNFpred

-ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNRLKYALTGDEVKKICMQRFIKIDGKVRVDVTYPAGFMDVISIEKTGEHFRLVYDTKGRFAVHRI

6az1E2

0.61

0.58

16.59

1.33

DEthreader

--A--KKHLKRLYAPKDWML-SKLGVFAPRPRPGPHKLRECLPLLVIIRNRLKYALNAREGEMILRQGLVHVDNHPRRDGKYPAGFMDVVEIPKTGDRFRLMYDVKGRFALVSL

(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	0.8177

(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	3j38E2	0.97	0.75	0.807	1.000	model1_3j38E2.pdb.gz
2	6ybwC1	0.96	0.94	1.000	0.991	model1_6ybwC1.pdb.gz
3	6zmtE	0.96	0.92	1.000	0.991	model1_6zmtE.pdb.gz
4	3j7aF	0.96	1.14	0.646	0.991	model1_3j7aF.pdb.gz
5	6zu9S	0.96	0.92	0.796	0.991	model1_6zu9S.pdb.gz
6	5xyiE	0.95	1.07	0.611	0.991	model1_5xyiE.pdb.gz
7	5xxuE	0.95	0.91	0.732	0.983	model1_5xxuE.pdb.gz
8	2xzmW1	0.94	1.29	0.549	0.991	model1_2xzmW1.pdb.gz
9	3j20E	0.89	1.38	0.398	0.983	model1_3j20E.pdb.gz
10	3izbD1	0.55	1.85	0.732	0.623	model1_3izbD1.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:0003735	0.99	structural constituent of ribosome
GO:1901363	0.51	heterocyclic compound binding
GO:0097159	0.51	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:1901564	1.00	organonitrogen compound metabolic process
GO:0044271	1.00	cellular nitrogen compound biosynthetic process
GO:0044267	1.00	cellular protein metabolic process
GO:0034645	1.00	cellular macromolecule biosynthetic process
GO:0006412	0.99	translation

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:0044444	1.00	cytoplasmic part
GO:0030529	1.00	intracellular ribonucleoprotein complex
GO:0044391	0.98	ribosomal subunit
GO:0022627	0.97	cytosolic small ribosomal subunit

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	3hbdA	0.447	4.47	0.052	0.816	3.2.1.14	NA
2	0.060	1cb8A	0.465	4.25	0.054	0.763	4.2.2.5	NA
3	0.060	2dkvA	0.438	4.83	0.093	0.877	3.2.1.14	40
4	0.060	2q85A	0.443	4.92	0.076	0.860	1.1.1.158	NA
5	0.060	2z38A	0.448	4.35	0.040	0.825	3.2.1.14	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	0.02	1i97D	0.521	3.62	0.103	0.737	0.26	TAC	complex1.pdb.gz	83,85,89
2	0.01	1h3f0	0.491	2.63	0.118	0.623	0.19	III	complex2.pdb.gz	31,33,34,36
3	0.01	3nanA	0.388	4.66	0.010	0.702	0.10	HZ1	complex3.pdb.gz	43,44,47,54,72,73,74,103
4	0.01	2eatA	0.419	4.86	0.097	0.798	0.16	CZA	complex4.pdb.gz	32,34,42
5	0.01	2eauA	0.396	4.79	0.058	0.719	0.13	CZA	complex5.pdb.gz	36,72,73
6	0.01	3b9rB	0.394	4.73	0.028	0.719	0.20	ACP	complex6.pdb.gz	71,72,89
7	0.01	2c88A	0.394	4.65	0.049	0.702	0.20	ACP	complex7.pdb.gz	85,99,100
8	0.01	3fgoA	0.397	4.61	0.028	0.711	0.17	CZA	complex8.pdb.gz	73,76,83,84

	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.