D-I-TASSER O95251-D3

D-I-TASSER results for O95251-D3

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

Input Sequence in FASTA format

>O95251 (128 residues)
GQITEGSNMIKTIAFGRYELDTWYHSPYPEEYARLGRLYMCEFCLKYMKSQTILRRHMAK
CVWKHPPGDEIYRKGSISVFEVDGKKNKIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVMT
EADNTGCH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| GQITEGSNMIKTIAFGRYELDTWYHSPYPEEYARLGRLYMCEFCLKYMKSQTILRRHMAKCVWKHPPGDEIYRKGSISVFEVDGKKNKIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVMTEADNTGCH
Prediction	CCCCCCCCCCCSSSSCCSSSSCCCCCCCCHHHCCCCCSSSCCCHHHHHCCHHHHHHHHHCCCCCCCCCCSSSSCCCSSSSSSSCCCCHHHHHHHHHHHHHHHCCCSSSSSCCCSSSSSSSSSCCCCCC
Confidence	97556788877799867788257489997234379927981021335299999999982188989997578864986699993886615788999999986215304650687389999995699889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| GQITEGSNMIKTIAFGRYELDTWYHSPYPEEYARLGRLYMCEFCLKYMKSQTILRRHMAKCVWKHPPGDEIYRKGSISVFEVDGKKNKIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVMTEADNTGCH
Prediction	86445455405302014230411140222641572630100320041154442043235405463031420145761101102355443104200200211143210222243120000012376328
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCSSSSCCSSSSCCCCCCCCHHHCCCCCSSSCCCHHHHHCCHHHHHHHHHCCCCCCCCCCSSSSCCCSSSSSSSCCCCHHHHHHHHHHHHHHHCCCSSSSSCCCSSSSSSSSSCCCCCC
GQITEGSNMIKTIAFGRYELDTWYHSPYPEEYARLGRLYMCEFCLKYMKSQTILRRHMAKCVWKHPPGDEIYRKGSISVFEVDGKKNKIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVMTEADNTGCH

2ou2A

0.61

0.57

16.34

1.33

DEthreader

-----K--NIECIELGRHRLKPWYFSPYPQELTTLPVLYLCEFCLKYGRSLKCLQRHLTKCDLRHPPGNEIYRKGTISFFEIDGRKNKSYSQNLCLLAKCFLDHTLYYD-TDPFLFYVMTEYDCKGFH

2pq8A1

0.60

0.57

16.34

5.50

SPARKS-K

-------KYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHRTLYFDVEPFVFYILTEVDRQGAH

5gk9A1

1.00

0.94

26.25

1.42

MapAlign

--------MIKTIAFGRYELDTWYHSPYPEEYARLGRLYMCEFCLKYMKSQTILRRHMAKCVWKHPPGDEIYRKGSISVFEVDGKKNKIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVMTEADNTGCH

5gk9A

1.00

0.94

26.25

1.52

CEthreader

--------MIKTIAFGRYELDTWYHSPYPEEYARLGRLYMCEFCLKYMKSQTILRRHMAKCVWKHPPGDEIYRKGSISVFEVDGKKNKIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVMTEADNTGCH

5gk9A

1.00

0.94

26.25

3.25

MUSTER

--------MIKTIAFGRYELDTWYHSPYPEEYARLGRLYMCEFCLKYMKSQTILRRHMAKCVWKHPPGDEIYRKGSISVFEVDGKKNKIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVMTEADNTGCH

1fy7A

0.50

0.48

14.05

4.31

HHsearch

----ARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRKKCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLDHKTLYYDVDPFLFYCMTRRDELGHH

2pq8A1

0.60

0.57

16.34

2.22

FFAS-3D

-------KYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHRTLYFDVEPFVFYILTEVDRQGAH

5gk9A1

0.97

0.91

25.40

1.33

EigenThreader

--------MIKTIAFGRYELDTWYHSPYPEEYARLGRLYMCEFCLKYMKSQTILRRHMAKCVWKHPPGDEIYRKGSISVFEVDGKKNKIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVMTEADN-TGC

5gk9A

1.00

0.94

26.25

3.21

CNFpred

--------MIKTIAFGRYELDTWYHSPYPEEYARLGRLYMCEFCLKYMKSQTILRRHMAKCVWKHPPGDEIYRKGSISVFEVDGKKNKIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVMTEADNTGCH

2rc4A

0.72

0.68

19.30

1.33

DEthreader

-------RCPSVIEFGKYEIHTWYSSPYPQEYSRLPKLYLCEFCLKYMKSRTILQQHMKKCGWFHPPANEIYRKNNISVFEVDGNVSTIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVLTQNDVKGCH

(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	0.8011

(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	5gk9A1	0.92	0.52	1.000	0.938	model1_5gk9A1.pdb.gz
2	2rc4A	0.92	0.81	0.719	0.945	model1_2rc4A.pdb.gz
3	2ou2A	0.91	0.89	0.642	0.938	model1_2ou2A.pdb.gz
4	2pq8A1	0.90	1.04	0.603	0.945	model1_2pq8A1.pdb.gz
5	1fy7A	0.87	1.44	0.504	0.945	model1_1fy7A.pdb.gz
6	3e4cA	0.34	5.08	0.043	0.656	model1_3e4cA.pdb.gz
7	1kmhA	0.34	5.26	0.033	0.648	model1_1kmhA.pdb.gz
8	2pr1A	0.32	4.63	0.061	0.586	model1_2pr1A.pdb.gz
9	4k68A	0.31	5.35	0.043	0.594	model1_4k68A.pdb.gz
10	3eoqB2	0.30	4.70	0.043	0.547	model1_3eoqB2.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	0.92	catalytic activity
GO:0004402	0.91	histone acetyltransferase activity
GO:1901363	0.61	heterocyclic compound binding
GO:0097159	0.61	organic cyclic compound binding
GO:0008134	0.55	transcription factor binding
GO:0003676	0.50	nucleic acid 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:0071704	0.96	organic substance metabolic process
GO:0044238	0.96	primary metabolic process
GO:0044237	0.96	cellular metabolic process
GO:0044260	0.95	cellular macromolecule metabolic process
GO:0016043	0.90	cellular component organization
GO:0006325	0.89	chromatin organization
GO:0016570	0.88	histone modification
GO:0016573	0.85	histone acetylation
GO:0065007	0.83	biological regulation
GO:0050789	0.83	regulation of biological process
GO:0050794	0.76	regulation of cellular process
GO:0019222	0.73	regulation of metabolic process
GO:0060255	0.72	regulation of macromolecule metabolic process
GO:0009889	0.70	regulation of biosynthetic process
GO:0080090	0.69	regulation of primary metabolic process
GO:0031323	0.69	regulation of cellular metabolic process
GO:0010468	0.69	regulation of gene expression
GO:2000112	0.68	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.68	regulation of nucleobase-containing compound metabolic process
GO:0048518	0.67	positive regulation of biological process
GO:0006355	0.66	regulation of transcription, DNA-templated
GO:0044699	0.58	single-organism process
GO:0048522	0.57	positive regulation of cellular process
GO:0048523	0.56	negative regulation of cellular process
GO:0034641	0.55	cellular nitrogen compound metabolic process
GO:1902680	0.54	positive regulation of RNA biosynthetic process
GO:0090304	0.54	nucleic acid metabolic process
GO:0010628	0.54	positive regulation of gene expression
GO:0045893	0.53	positive regulation of transcription, DNA-templated
GO:0044763	0.53	single-organism cellular 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:0043229	0.89	intracellular organelle
GO:0044446	0.86	intracellular organelle part
GO:0044428	0.84	nuclear part
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0005634	0.81	nucleus
GO:0032991	0.74	macromolecular complex
GO:0043234	0.67	protein complex
GO:1902494	0.63	catalytic complex
GO:0044451	0.63	nucleoplasm part
GO:1990234	0.62	transferase complex
GO:0000123	0.61	histone acetyltransferase 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	0.082	2pq8A	0.903	1.04	0.603	0.945	2.3.1.48	121
2	0.067	1fy7A	0.871	1.44	0.504	0.945	2.3.1.48	NA
3	0.060	3c6gB	0.420	4.70	0.085	0.703	1.14.13.15	96
4	0.060	2fj0A	0.427	5.15	0.048	0.844	3.1.1.1	NA
5	0.060	1e39A	0.439	3.95	0.050	0.648	1.3.99.1	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	0.01	2quvA	0.316	4.93	0.049	0.586	0.72	PO4	complex1.pdb.gz	14,15,16,41,42

	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.