D-I-TASSER Q7Z5K2-D4

D-I-TASSER results for Q7Z5K2-D4

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

Input Sequence in FASTA format

>Q7Z5K2 (75 residues)
MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTT
GQKSISRVIEYLEHC

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC
Prediction	CCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCC
Confidence	961289999999999998159889999999889997799999999999999997246642168999999998639
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC
Prediction	864222222202100100342752254037304754154015105412412432344566436204402632677
	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

                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCC
MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC

4k6jA3

1.00

28.00

1.33

DEthreader

MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC

4k6jA3

1.00

28.00

1.40

SPARKS-K

MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC

4k6jA3

1.00

28.00

1.24

MapAlign

MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC

4k6jA

1.00

28.00

0.87

CEthreader

MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC

4k6jA3

1.00

28.00

1.20

MUSTER

MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC

4k6jA3

1.00

28.00

2.44

HHsearch

MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC

4k6jA3

1.00

28.00

1.59

FFAS-3D

MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC

4k6jA3

1.00

28.00

0.77

EigenThreader

MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC

4k6jA

1.00

28.00

0.92

CNFpred

MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC

4k6jA

1.00

28.00

1.33

DEthreader

MEDCIVASYTALLLGCLCQESPINVTTVREYLPEGDFSIMTEMLKKFLSFMNLTCAVGTTGQKSISRVIEYLEHC

(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	0.7981

(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	4k6jA	0.99	0.24	1.000	1.000	model1_4k6jA.pdb.gz
2	3qsgA	0.66	2.67	0.058	0.907	model1_3qsgA.pdb.gz
3	6gym03	0.66	2.89	0.070	0.947	model1_6gym03.pdb.gz
4	1i36A2	0.65	2.48	0.103	0.880	model1_1i36A2.pdb.gz
5	5je8A2	0.65	2.63	0.085	0.907	model1_5je8A2.pdb.gz
6	2qfnA	0.65	3.01	0.082	0.960	model1_2qfnA.pdb.gz
7	3dojA	0.64	2.82	0.058	0.920	model1_3dojA.pdb.gz
8	2uyyA	0.64	2.80	0.057	0.920	model1_2uyyA.pdb.gz
9	1yb4A	0.63	2.51	0.058	0.893	model1_1yb4A.pdb.gz
10	3pefA2	0.63	2.70	0.058	0.907	model1_3pefA2.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	0.55	heterocyclic compound binding
GO:0097159	0.55	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:0071922	1.00	regulation of cohesin loading
GO:0060623	1.00	regulation of chromosome condensation
GO:0045132	1.00	meiotic chromosome segregation
GO:0007064	1.00	mitotic sister chromatid cohesion

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:0044428	1.00	nuclear part
GO:0044427	0.95	chromosomal part
GO:0043234	0.95	protein complex
GO:0000798	0.93	nuclear cohesin complex
GO:0043226	0.58	organelle
GO:0043229	0.56	intracellular organelle

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	1bmtA	0.588	2.66	0.042	0.867	2.1.1.13	NA
2	0.060	1cqxB	0.581	3.23	0.096	0.933	1.14.12.17	NA
3	0.060	2pfdB	0.619	2.88	0.045	0.880	2.1.2.5 4.3.1.4	NA
4	0.060	2iewB	0.611	3.73	0.053	0.960	2.7.1.151	NA
5	0.060	1dkpA	0.586	3.48	0.028	0.920	3.1.3.2 3.1.3.26	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	0.24	2c7lA	0.627	2.86	0.108	0.867	0.33	BLA	complex1.pdb.gz	7,8,10,11,15,27,35
2	0.08	2j96B	0.624	2.78	0.119	0.880	0.33	PVN	complex2.pdb.gz	36,40,41,72
3	0.07	2c7kA	0.621	2.51	0.119	0.867	0.38	BLA	complex3.pdb.gz	16,28,35,39,40
4	0.06	3lb3B	0.649	3.16	0.082	0.973	0.36	HEM	complex4.pdb.gz	7,10,11,13,14,28,31,32,35
5	0.06	3oj1B	0.650	3.00	0.082	0.973	0.31	HEM	complex5.pdb.gz	14,26,31,32,35,39,40,43,72
6	0.02	2j960	0.623	2.85	0.104	0.880	0.25	III	complex6.pdb.gz	42,46,48,49,52,58,61,62,65,66,69,70
7	0.01	2uyyA	0.637	2.80	0.057	0.920	0.11	NA7	complex7.pdb.gz	13,14,32
8	0.01	1all0	0.621	2.85	0.074	0.893	0.14	III	complex8.pdb.gz	9,16,19,20,22
9	0.01	2vjt0	0.624	3.01	0.044	0.893	0.26	III	complex9.pdb.gz	24,35,36,47

	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.