D-I-TASSER Q9HAD4-D2

D-I-TASSER results for Q9HAD4-D2

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

Input Sequence in FASTA format

>Q9HAD4 (137 residues)
NGHTQKITAIITFPSLESCEEKNQLILTASADRTVIVWDGDTTRQVQRISCFQSTVKCLT
VLQRLDVWLSGGNDLCVWNRKLDLLCKTSHLSDTGISALVEIPKNCVVAAVGKELIIFRL
VAPTEGSLEWDILEVKR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| NGHTQKITAIITFPSLESCEEKNQLILTASADRTVIVWDGDTTRQVQRISCFQSTVKCLTVLQRLDVWLSGGNDLCVWNRKLDLLCKTSHLSDTGISALVEIPKNCVVAAVGKELIIFRLVAPTEGSLEWDILEVKR
Prediction	CCCCCCSSSSSSSCCCCCCCCCCCSSSSSSCCCCSSSSSCCCCCSSSSSCCCCCCSSSSSSSCCCCSSSSCCCCSSSSSCCCCSSSSSCCCCCCCSSSSSSCCCCSSSSSSCCCSSSSSSSCCCCCSSSSSSSCSCC
Confidence	99888778999965866778899899999389909997789992999991789978999992999989985896899968899899961777886899999399969999689879999976998527676220139
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| NGHTQKITAIITFPSLESCEEKNQLILTASADRTVIVWDGDTTRQVQRISCFQSTVKCLTVLQRLDVWLSGGNDLCVWNRKLDLLCKTSHLSDTGISALVEIPKNCVVAAVGKELIIFRLVAPTEGSLEWDILEVKR
Prediction	86654401000011344445553300000244310204227434112304414430200000453431002331010013634211414434423010003157320000134412002031556432413134258
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCSSSSSSSCCCCCCCCCCCSSSSSSCCCCSSSSSCCCCCSSSSSCCCCCCSSSSSSSCCCCSSSSCCCCSSSSSCCCCSSSSSCCCCCCCSSSSSSCCCCSSSSSSCCCSSSSSSSCCCCCSSSSSSSCSCC
NGHTQKITAIITFPSLESCEEKNQLILTASADRTVIVWDGDTTRQVQRISCFQSTVKCLTVLQRLDVWLSGGNDLCVWNRKLDLLCKTSHLSDTGISALVEIPKNCVVAAVGKELIIFRLVAPTEGSLEWDILEVKR

4j87A

0.13

0.12

4.29

1.33

DEthreader

DGHDGPVRGIAFHPT-------QPIFVSGGDDYKVNVWNYKSRKLLFSLCGHMDYVRVCTFHHEYPWILSCSDTIRIWNWQSRNCIAILTGHSHYVMCAAFHPSDLIVSASLQTVRVWDISGRKN-AADAIVFVLEG

5yzvA2

0.18

0.16

5.24

1.69

SPARKS-K

-GHTDYVYAVAFSPD-------GSMVASGSRDGTIRLWDVATGKERDVLQAPAENVVSLAFSPDGSMLVHGSDTVHLWDVASGEALHTFEGHTDWVRAVAFSPDGALLASGSDDIRLWDVATTLEGHTEPVH-----

6zu9l1

0.12

4.09

0.29

MapAlign

-GHERPLTQVKYN-------KEGDLLFSCSKDSSASVWYSLNGERLGTLDGHTGTIWSIDVDCFTKYCVTGSASIKLWDVSNGQCVATWKSP-VPVKRVEFSCGNYFLAILDGSINIYEIERDSATHELVSPIHKII

4d6vA

0.22

0.20

6.43

0.26

CEthreader

DGHTEWVSCVRFSPNP-----ALPVIISAGWDKTVKVWELSNCKLKTTHHGHTGYLNTLAVSPDGSLAASGGKDTMLWDLNEGKHLYSLDAG-DVINALVFSPNRWLCAATASSIKIFDL------ESKSLVDDLQP

5cvlA

0.20

0.19

6.07

1.24

MUSTER

SGNKDSIYSLAMNQL-------GTIIVSGSTEKVLRVWDPRTCAKLMKLKGHTDNVKALLLNRDGTQCLSGSSDIRLWSLGQQRCIATYRVHDEGVWALQVNDAFTHVYSGGRD-RKIYCTDLRNPDIRVLICEEKA

3dm0A

0.16

0.15

4.88

0.63

HHsearch

TGHSHFVEDVVLSSD-------GQFALSGSWDGELRLWDLAAGVSTRRFVGHTKDVLSVAFSLDNRQIVSASRDIKLWNTL-GECKYTIEGHRDWVSCVRFSPNTLTIVSASKTVKVWNLSSTLAGHTGYVSTVAVS

4j87A1

0.23

0.19

5.95

1.56

FFAS-3D

AGHDRGVNWCAFHP-------TLPLILSAGDDRLVKLWRMTASKEVDTCRGHFNNVSCCLFHPHQELILSASEDIRVWDLNRRTAVQTFRRANDRFWFITVHPKLNLFAAAHDSVMVFKL-----------------

6yleA1

0.16

0.15

4.88

0.47

EigenThreader

-AHYQSITKIKSILN-------GKYIITSGNDSRVIIWQTVDPKPLCILHDHTLPVTDFQVSSSDTKLFTVSQTIRCYDLSLPVLLATFTT-PYSIKSIVLDPADRACYIGTAGCFSLNLFSLQRLYAMGQLVCNVL

5cvoA

0.20

0.18

5.84

1.92

CNFpred

SGNKDSIYSLAMNQLG-------TIIVSGSTEKVLRVWDPRTCAKLMKLKGHTDNVKALLLNRDGTQCLSGSSTIRLWSLGQQRCIATYRVHDEGVWALQVNDAFTHVYSGGRKIYCTDLRNP-----DIRVLICEE

3fm0A

0.18

5.68

1.33

DEthreader

NSHTQDVKHVVWHPSQ-------ELLASASYDDTVKLYREDDWVCCATLEGHESTVWSLAFDPSGQRLASCSDTVRIWRQYSWKCICTLSFHSRTIYDIAWCQTGALATACGDAIRVFQEDPSDPQQPTFSLTHLHA

(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	0.8173

(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	6tblE	0.87	1.59	0.154	0.949	model1_6tblE.pdb.gz
2	6f3tA2	0.87	1.74	0.154	0.949	model1_6f3tA2.pdb.gz
3	3zwlB	0.87	1.62	0.147	0.942	model1_3zwlB.pdb.gz
4	4wjsA	0.86	1.69	0.169	0.949	model1_4wjsA.pdb.gz
5	6jp6A1	0.86	1.98	0.075	0.971	model1_6jp6A1.pdb.gz
6	3i2nA	0.86	1.96	0.075	0.971	model1_3i2nA.pdb.gz
7	4j87A	0.85	1.29	0.167	0.920	model1_4j87A.pdb.gz
8	2h9lA	0.85	1.09	0.179	0.898	model1_2h9lA.pdb.gz
9	6t9iD2	0.85	2.10	0.169	0.949	model1_6t9iD2.pdb.gz
10	5yzvA	0.85	1.16	0.153	0.905	model1_5yzvA.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	0.70	catalytic activity
GO:0016740	0.58	transferase activity
GO:0061659	0.54	ubiquitin-like protein ligase activity
GO:0097159	0.51	organic cyclic compound binding
GO:1901363	0.50	heterocyclic 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:0009987	0.96	cellular process
GO:0071704	0.86	organic substance metabolic process
GO:0044237	0.86	cellular metabolic process
GO:0044238	0.85	primary metabolic process
GO:0043170	0.84	macromolecule metabolic process
GO:0044260	0.83	cellular macromolecule metabolic process
GO:0006807	0.71	nitrogen compound metabolic process
GO:0006139	0.70	nucleobase-containing compound metabolic process
GO:0090304	0.69	nucleic acid metabolic process
GO:0071840	0.69	cellular component organization or biogenesis
GO:0065007	0.68	biological regulation
GO:0044699	0.68	single-organism process
GO:0016043	0.67	cellular component organization
GO:0050789	0.66	regulation of biological process
GO:0050794	0.65	regulation of cellular process
GO:0019538	0.61	protein metabolic process
GO:0044763	0.59	single-organism cellular process
GO:0006464	0.58	cellular protein modification process
GO:0048518	0.56	positive regulation of biological process
GO:0016070	0.56	RNA metabolic process
GO:1901575	0.55	organic substance catabolic process
GO:0009057	0.54	macromolecule catabolic process
GO:0022402	0.53	cell cycle process
GO:0010498	0.53	proteasomal protein catabolic process
GO:0006996	0.53	organelle organization
GO:0070647	0.51	protein modification by small protein conjugation or removal
GO:0048522	0.50	positive regulation of cellular process
GO:0043933	0.50	macromolecular complex subunit organization
GO:0032446	0.50	protein modification by small protein conjugation

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:0044446	0.96	intracellular organelle part
GO:0016020	0.77	membrane
GO:0044444	0.69	cytoplasmic part
GO:0098588	0.61	bounding membrane of organelle
GO:0005774	0.60	vacuolar membrane
GO:0005765	0.56	lysosomal membrane
GO:0043227	0.52	membrane-bounded organelle
GO:0005634	0.50	nucleus

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	0.066	1rwlA	0.741	2.24	0.050	0.883	2.7.11.1	12
2	0.060	2fpcA	0.771	2.16	0.096	0.898	4.3.3.2	37
3	0.060	3fw0A	0.765	1.98	0.058	0.883	4.3.2.5	NA
4	0.060	3dr2A	0.741	1.99	0.076	0.869	3.1.1.17	NA
5	0.060	1w6sC	0.752	2.37	0.078	0.920	1.1.99.8	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	0.20	2xl3B	0.852	1.13	0.179	0.898	0.63	III	complex1.pdb.gz	55,72,97,112
2	0.20	3smrA	0.853	1.15	0.179	0.898	0.62	NP7	complex2.pdb.gz	7,8,9,57,95,97,112
3	0.20	3eg6A	0.849	1.17	0.179	0.898	0.61	III	complex3.pdb.gz	6,8,31,55,56,57,73,97,112
4	0.04	1a0rB	0.832	1.35	0.138	0.898	0.71	FAR	complex4.pdb.gz	89,96,109,111,114,116,118

	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.