D-I-TASSER Q7Z4Q2-D4

D-I-TASSER results for Q7Z4Q2-D4

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

Input Sequence in FASTA format

>Q7Z4Q2 (149 residues)
SQCMTPDQLMTLCKAGIHSSNVGVRVNVVSILGITGSVLAKEDGTLETLKNIGCFLLEVT
TKDPSLVVAGEALDALFDVFADGKEAERASIQIKLLSALKEFQPVFKMKIRKEGRGNYST
DQLCVLDNVKMNLRRFIAYQETVEKRLTS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| SQCMTPDQLMTLCKAGIHSSNVGVRVNVVSILGITGSVLAKEDGTLETLKNIGCFLLEVTTKDPSLVVAGEALDALFDVFADGKEAERASIQIKLLSALKEFQPVFKMKIRKEGRGNYSTDQLCVLDNVKMNLRRFIAYQETVEKRLTS
Prediction	CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence	99899999999999863079888999999999999998615888599999999999999468998999999999997662499853789998078999999999999999987411476889999999999999999999998432169
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| SQCMTPDQLMTLCKAGIHSSNVGVRVNVVSILGITGSVLAKEDGTLETLKNIGCFLLEVTTKDPSLVVAGEALDALFDVFADGKEAERASIQIKLLSALKEFQPVFKMKIRKEGRGNYSTDQLCVLDNVKMNLRRFIAYQETVEKRLTS
Prediction	85424572043015205627345021200100010031224473325103300310041036553121002022000000134624440135350063046015303620452547634553241053033004200511564466358
	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                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
SQCMTPDQLMTLCKAGIHSSNVGVRVNVVSILGITGSVLAKEDGTLETLKNIGCFLLEVTTKDPSLVVAGEALDALFDVFADGKEAERASIQIKLLSALKEFQPVFKMKIRKEGRGNYSTDQLCVLDNVKMNLRRFIAYQETVEKRLTS

4gmnA

0.19

0.18

5.83

1.33

DEthreader

KLTPTDNPHRKFISLYHSSKQPGLGVKCIGVVGSLAH--D-P-APIEVNREVGVFLVTLLQSNVPPAEIVEALNQLFDIYGDEEADKEVFWKDGFLKHLEEFLPKMRTLTKGIDKRT-QPELRTRADEALLNLGRFVQYKKKHA-----

4gmnA4

0.19

0.18

5.83

1.53

SPARKS-K

ETPTDGNPHRKFISLYHSSKFQGLGVKCIGVVGSL----AHDPAPIEVNREVGVFLVTLLRQNVPPAEIVEALNQLFDIYGDEELDKEVFWKDGFLKHLEEFLPKMRTLTKGIDKRT-QPELRTRADEALLNLGRFVQYKKKHA-----

6u1sA1

0.06

0.05

2.39

0.71

MapAlign

AELA-KKAIEAIYRLADNHTTDTFMAKAIEAIAELAKEAIKIAAIAELARKAIDAIYRLARNHTTDTFMAKAIEAIAELAKE--AIKAIAISA-IAELARKAIEAILRLASNL----TSETYMRKAQEAIEKIARTAEEAIRDLARNL-

4gmnA4

0.19

0.17

5.64

0.51

CEthreader

ETPTDGNPHRKFISLYHSSKFQGLGVKCIGVVGSLAH----DPAPIEVNREVGVFLVTLLRQSVPPAEIVEALNQLFDIYGDEACDKEVFWKDGFLKHLEEFLPKMRTLTKGIDKRT-QPELRTRADEALLNLGRFVQYKKKHA-----

4gmnA4

0.19

0.18

5.83

1.47

MUSTER

ETPTDGNPHRKFISLYHSSPFQGLGVKCIGVVGSLAH----DPAPIEVNREVGVFLVTLLRQNVPPAEIVEALNQLFDIYGDEELAKEVFWKDGFLKHLEEFLPKMRTLTKGIDKRT-QPELRTRADEALLNLGRFVQYKKKHA-----

4gmnA4

0.21

0.19

6.19

3.90

HHsearch

ETPTDGNPHRKFISLYHSSPFQGLGVKCIGVVGS----LAHDPAPIEVNREVGVFLVTLLRQSVPPAEIVEALNQLFDIYGDEELACEVFWKDGFLKHLEEFLPKMRTLTKGIDKRT-QPELRTRADEALLNLGRFVQYKKKHA-----

4gmnA4

0.21

0.19

5.98

1.96

FFAS-3D

---TDGNPHRKFISLYHSSKQQGLGVKCIGVVGSL----AHDPAPIEVNREVGVFLVTLLRQNVPPAEIVEALNQLFDIYGDEELACDVFWKDGFLKHLEEFLPKMRTLTKGIDKRT-QPELRTRADEALLNLGRFVQYKKKH------

4gmnA4

0.19

0.18

5.85

0.72

EigenThreader

HGETPTNPHRKFISLYHSSKQDPFQGLGVKCIGVVGSLAH-DPAPIEVNREVGVFLVTLLRQSVPPAEIVEALNQLFDIYGDEACDKEVFWKDGFLKHLEEFLPKMRTLTKGI-DKRTQPELRTRADEALLNLGRFVQYKKKHA-----

4gmoA

0.19

0.17

5.64

0.97

CNFpred

ETPTDGNPHRKFISLYHSSK-QGLGVKCIGVVGSLAHD----PAPIEVNREVGVFLVTLLRQSVPPAEIVEALNQLFDIYGDEACDKEVFWKDGFLKHLEEFLPKMRTLTKGIDKR-TQPELRTRADEALLNLGRFVQYKKKHAP----

4gmnA4

0.19

0.18

5.83

1.33

DEthreader

LETPTDNPHRKFISLYHSSKQPGLGVKCIGVVGSLAH--D-P-APIEVNREVGVFLVTLLQSNVPPAEIVEALNQLFDIYGDEEADKEVFWKDGFLKHLEEFLPKMRTLTKGIDKRT-QPELRTRADEALLNLGRFVQYKKKHA-----

(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	0.8485

(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	4gmnA4	0.87	1.57	0.187	0.933	model1_4gmnA4.pdb.gz
2	5vchA3	0.76	2.34	0.094	0.899	model1_5vchA3.pdb.gz
3	6u1sA	0.73	3.26	0.088	0.980	model1_6u1sA.pdb.gz
4	3w3tA	0.72	3.01	0.083	0.933	model1_3w3tA.pdb.gz
5	4hm9A	0.72	2.82	0.101	0.913	model1_4hm9A.pdb.gz
6	1qgkA1	0.68	2.88	0.090	0.886	model1_1qgkA1.pdb.gz
7	1qbkB2	0.64	3.02	0.110	0.832	model1_1qbkB2.pdb.gz
8	1b3uA	0.62	3.05	0.087	0.819	model1_1b3uA.pdb.gz
9	3f3fD	0.44	4.32	0.047	0.718	model1_3f3fD.pdb.gz
10	2yvzA	0.44	3.71	0.146	0.644	model1_2yvzA.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	0.59	heterocyclic compound binding
GO:0097159	0.59	organic cyclic compound binding
GO:0022892	0.53	substrate-specific transporter activity
GO:0005048	0.53	signal sequence binding
GO:0051082	0.50	unfolded 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:0071840	0.95	cellular component organization or biogenesis
GO:0044699	0.95	single-organism process
GO:1902578	0.94	single-organism localization
GO:0072594	0.94	establishment of protein localization to organelle
GO:0033365	0.94	protein localization to organelle
GO:0006886	0.94	intracellular protein transport
GO:0009987	0.88	cellular process
GO:0071704	0.83	organic substance metabolic process
GO:0044237	0.83	cellular metabolic process
GO:0044260	0.82	cellular macromolecule metabolic process
GO:0044238	0.82	primary metabolic process
GO:0065007	0.78	biological regulation
GO:0006606	0.76	protein import into nucleus
GO:0043412	0.72	macromolecule modification
GO:0006996	0.72	organelle organization
GO:0006464	0.71	cellular protein modification process
GO:0050794	0.63	regulation of cellular process
GO:0080090	0.58	regulation of primary metabolic process
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0031323	0.58	regulation of cellular metabolic process
GO:0043933	0.56	macromolecular complex subunit organization
GO:0034622	0.55	cellular macromolecular complex assembly
GO:0031399	0.55	regulation of protein modification process
GO:0070647	0.54	protein modification by small protein conjugation or removal
GO:0018205	0.54	peptidyl-lysine modification
GO:1903320	0.53	regulation of protein modification by small protein conjugation or removal
GO:0071427	0.53	mRNA-containing ribonucleoprotein complex export from nucleus
GO:0051783	0.53	regulation of nuclear division
GO:0051028	0.53	mRNA transport
GO:0043623	0.53	cellular protein complex assembly
GO:0030162	0.53	regulation of proteolysis
GO:0022613	0.53	ribonucleoprotein complex biogenesis
GO:0016926	0.53	protein desumoylation
GO:0010564	0.53	regulation of cell cycle process
GO:0010467	0.53	gene expression
GO:0007346	0.53	regulation of mitotic cell cycle
GO:0007067	0.53	mitotic nuclear division
GO:0006405	0.53	RNA export from nucleus
GO:0042273	0.50	ribosomal large subunit biogenesis

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	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0043229	0.95	intracellular organelle
GO:0043231	0.91	intracellular membrane-bounded organelle
GO:0032991	0.88	macromolecular complex
GO:0043234	0.86	protein complex
GO:0044444	0.84	cytoplasmic part
GO:0044446	0.83	intracellular organelle part
GO:0005634	0.81	nucleus
GO:0044428	0.77	nuclear part
GO:0005829	0.61	cytosol

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	1g87B	0.602	3.37	0.074	0.826	3.2.1.4	NA
2	0.060	1hn0A	0.579	3.86	0.072	0.859	4.2.2.20	NA
3	0.060	1dl2A	0.604	3.66	0.092	0.866	3.2.1.113	NA
4	0.060	2vn4A	0.597	4.21	0.027	0.940	3.2.1.3	NA
5	0.060	1hcuB	0.589	3.77	0.083	0.899	3.2.1.113	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	0.08	3c2gA	0.703	2.98	0.138	0.926	0.65	III	complex1.pdb.gz	70,78,81,82,87,135,139,142
2	0.08	2bptA	0.684	2.83	0.090	0.873	0.86	III	complex2.pdb.gz	32,34,37,38,71,74
3	0.07	1bk6B	0.643	3.15	0.119	0.846	0.63	III	complex3.pdb.gz	33,36,52,71,75,129,132
4	0.02	1f59B	0.676	2.99	0.090	0.886	0.69	III	complex4.pdb.gz	36,82,83,84,85,88,89
5	0.02	1f59B	0.676	2.99	0.090	0.886	0.66	III	complex5.pdb.gz	50,54,57,58
6	0.02	1o6pA	0.679	3.05	0.090	0.893	0.64	III	complex6.pdb.gz	52,85,88,89
7	0.02	1o6oA	0.677	2.95	0.090	0.886	0.61	III	complex7.pdb.gz	53,86,89,94,95
8	0.02	2l1lB	0.528	3.23	0.101	0.732	0.63	III	complex8.pdb.gz	5,12,22,25,26,29,31,45,47,48,51,52,55,60,64,65,68
9	0.01	1qgk1	0.209	2.78	0.070	0.242	0.65	III	complex9.pdb.gz	25,26,29,30,33,36,37,38,41

	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.