D-I-TASSER Q9C0D6-D9

D-I-TASSER results for Q9C0D6-D9

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

Input Sequence in FASTA format

>Q9C0D6 (103 residues)
SMSSGVGEMGDSQVSSNPTSSPPGEAPAPVSVDSEPSCKGGLPRDKPTKRKDVVAPKRGS
LKEASPGASKPGSARRSQGAVAKSVRTLTASENESMRKVMPIT

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| SMSSGVGEMGDSQVSSNPTSSPPGEAPAPVSVDSEPSCKGGLPRDKPTKRKDVVAPKRGSLKEASPGASKPGSARRSQGAVAKSVRTLTASENESMRKVMPIT
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCC
Confidence	9888888778888888988889877788878888865578999886567775788887875657999999888888988888863146876553542001079
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| SMSSGVGEMGDSQVSSNPTSSPPGEAPAPVSVDSEPSCKGGLPRDKPTKRKDVVAPKRGSLKEASPGASKPGSARRSQGAVAKSVRTLTASENESMRKVMPIT
Prediction	8456666545645347455445556444554475554665434675436556446446444564465445545454764444433432456535324423548
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCC
SMSSGVGEMGDSQVSSNPTSSPPGEAPAPVSVDSEPSCKGGLPRDKPTKRKDVVAPKRGSLKEASPGASKPGSARRSQGAVAKSVRTLTASENESMRKVMPIT

1h7zA

0.10

3.62

0.56

CEthreader

EANCIIEYGKQNPDSKLTLILVNGYVTLMGASDYVNTLFKNKNVSIYFDATGHILPDSSSLKTDSTTAYPFVLPNAGTHNENYIFGQCYYKASDGALFPLEVT

5m41A2

0.05

2.31

0.53

EigenThreader

LDLTAAQKRGAELSGMGGTISKSNPNGNVSPNEPGNPYAGEEFDFRLQHKDDNPYSFGNEMEWLVRKFKTKKNDFDLKDIPDNIHFRTDREKGPDTLFLDVAS

7kwzA

0.13

0.12

4.07

0.33

FFAS-3D

GLGNNQGSNNFGAFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGNNQNQGNMQREPNQAFGSGNNSYSGSNSGAAIGWGSAS-NAGSGSGF-------

5dfzB

0.13

4.40

1.27

SPARKS-K

NVFVQLEPTSYHMHSPNHGLKDNANVKPERKVVVSNSYEGDVESIEKFLSTFKILPPLRDYKE-FGPIQEIVRSPNMGNLRGKLIATLMENEPNSITSSAVSP

4uirA

0.24

0.05

1.51

0.42

CNFpred

----------------------------------------------------------------------------------TLVKDLDIHINTEGKVVEGII

1c1zA

0.03

1.63

0.83

DEthreader

-FSTSCYVS--RGGMRK--FICWPNTLKCTPR---FAGILENCAPIICPP-PSIPTFLHA--REVK-CPNWAMPSCKHG-DKVSFFCKNKEKK---YTECFKE

2oajA

0.10

3.62

0.63

MapAlign

ILMVCGTDMGEVITYKILPASGGKFDVQLMDITNVTSKGPIHKIDAFSKETKSSCGFDDIRLITLGKSKSTHKGFKYPLAATGLSYISTVEKNNDRKNLTVII

2nbiA2

0.13

0.12

4.06

0.80

MUSTER

SQPTGQPSSQPSECADVLELCPYDTCFLPFDDSSRPPDSVNRPDCDKLSTAIDFTCPTCCPTQCRPDNPSPSPDGSPPVCSPTMMPSPLPSPTE---------

2pffB

0.18

0.16

5.07

0.56

HHsearch

KAPSGLDQSR-IPFSERKLKFSNRFLPV----ASPFHSHLLVPASDLI-NKDL-------VKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISEGVRVIVAGT

3bq4A

0.05

2.31

0.52

CEthreader

PPNCQIVENTNTNDGKLTLVLVKNVGVSDTVNQMFTQKTANIQLRLYFDSSGNLLTEESDLKIPLKNKSSTATSTTRDSENYIHGICYYMTSYDRSLFPLNIS

(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	0.4087

(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	4heuA	0.44	3.48	0.052	0.680	model1_4heuA.pdb.gz
2	6ezuA	0.44	3.80	0.020	0.718	model1_6ezuA.pdb.gz
3	3jsiA1	0.44	4.07	0.051	0.728	model1_3jsiA1.pdb.gz
4	1aj8A	0.44	4.19	0.063	0.757	model1_1aj8A.pdb.gz
5	4i15A	0.44	4.16	0.039	0.728	model1_4i15A.pdb.gz
6	6chgB	0.43	4.30	0.049	0.806	model1_6chgB.pdb.gz
7	1xfjA	0.43	4.72	0.092	0.825	model1_1xfjA.pdb.gz
8	1sojL	0.43	4.28	0.019	0.728	model1_1sojL.pdb.gz
9	3v93A	0.42	4.04	0.071	0.718	model1_3v93A.pdb.gz
10	3ibjA3	0.40	4.03	0.039	0.709	model1_3ibjA3.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	0.74	catalytic activity
GO:0016787	0.73	hydrolase activity
GO:1901363	0.63	heterocyclic compound binding
GO:0097159	0.63	organic cyclic compound binding
GO:0016788	0.60	hydrolase activity, acting on ester bonds
GO:0017076	0.58	purine nucleotide binding
GO:0032555	0.57	purine ribonucleotide binding
GO:0030554	0.52	adenyl nucleotide binding
GO:0043169	0.51	cation binding
GO:0032559	0.51	adenyl ribonucleotide 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	0.95	cellular process
GO:0044763	0.94	single-organism cellular process
GO:0007017	0.86	microtubule-based process
GO:0006928	0.86	movement of cell or subcellular component
GO:0007018	0.85	microtubule-based movement
GO:0065007	0.53	biological regulation
GO:0050789	0.51	regulation of biological 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:0044464	0.99	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.80	cytoplasmic part
GO:0005737	0.74	cytoplasm
GO:0016020	0.69	membrane
GO:0005829	0.68	cytosol
GO:0043226	0.61	organelle
GO:0043229	0.52	intracellular organelle
GO:0043227	0.52	membrane-bounded 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	3eqmA	0.405	5.10	0.040	0.854	1.14.14.1	NA
2	0.060	3fzzA	0.406	4.61	0.036	0.748	3.4.21.-	NA
3	0.060	2q3zA	0.406	4.17	0.032	0.680	2.3.2.13	NA
4	0.060	1ofdA	0.361	4.54	0.078	0.689	1.4.7.1	NA
5	0.060	3h0lA	0.414	5.04	0.061	0.835	6.3.5.-	67

	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	0.01	3qpnA	0.420	3.94	0.052	0.699	0.19	PFK	complex1.pdb.gz	62,63,68,69,70,72,75
2	0.01	2weyA	0.433	4.03	0.061	0.718	0.14	EV1	complex2.pdb.gz	56,57,69
3	0.01	1t9sB	0.429	3.59	0.041	0.689	0.11	5GP	complex3.pdb.gz	41,42,67
4	0.01	1so2A	0.337	5.24	0.033	0.728	0.19	666	complex4.pdb.gz	57,58,68,69,70,72
5	0.01	1lm1A	0.394	4.33	0.061	0.718	0.10	FMN	complex5.pdb.gz	60,69,70,71,72
6	0.01	3hqzA	0.422	3.82	0.042	0.689	0.14	PF8	complex6.pdb.gz	83,84,86
7	0.01	3sieA	0.429	3.74	0.041	0.699	0.18	5BO	complex7.pdb.gz	55,59,65,68,70,71
8	0.01	3hqyA	0.423	3.81	0.042	0.689	0.15	PF6	complex8.pdb.gz	62,68,69,70,72,75
9	0.01	3lxgA	0.442	3.43	0.053	0.670	0.14	Z73	complex9.pdb.gz	67,69,72
10	0.01	1aj8A	0.437	4.19	0.063	0.757	0.18	COA	complex10.pdb.gz	61,67,68,69,70,71

	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.