D-I-TASSER Q6XZB0-D2

D-I-TASSER results for Q6XZB0-D2

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

Input Sequence in FASTA format

>Q6XZB0 (132 residues)
KFVDVIHSDSNGLGIQEPLGHIDFYPNGGNKQPGCPKSIFSGIQFIKCNHQRAVHLFMAS
LETNCNFISFPCRSYKDYKTSLCVDCDCFKEKSCPRLGYQAKLFKGVLKERMEGRPLRTT
VFLDTSGTYPFC

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| KFVDVIHSDSNGLGIQEPLGHIDFYPNGGNKQPGCPKSIFSGIQFIKCNHQRAVHLFMASLETNCNFISFPCRSYKDYKTSLCVDCDCFKEKSCPRLGYQAKLFKGVLKERMEGRPLRTTVFLDTSGTYPFC
Prediction	CCSSSSSSCCCCCCCCCSCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCSSSSCCCHHHHHHCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCSSSSSSSCCCCCCC
Confidence	946999938864677410453456379998899997765555313345448999999999637997237858899999828876677778887643582222222322344667887469999809999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| KFVDVIHSDSNGLGIQEPLGHIDFYPNGGNKQPGCPKSIFSGIQFIKCNHQRAVHLFMASLETNCNFISFPCRSYKDYKTSLCVDCDCFKEKSCPRLGYQAKLFKGVLKERMEGRPLRTTVFLDTSGTYPFC
Prediction	830000001133323342314232301324412314443443333220113001300020234734030240631630464444536445654112002204434444455456453403010404764368
	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

CCSSSSSSCCCCCCCCCSCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCSSSSCCCHHHHHHCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCSSSSSSSCCCCCCC
KFVDVIHSDSNGLGIQEPLGHIDFYPNGGNKQPGCPKSIFSGIQFIKCNHQRAVHLFMASLETNCNFISFPCRSYKDYKTSLCVDCDCFKEKSCPRLGYQAKLFKGVLKERMEGRPLRTTVFLDTSGTYPFC

6e7kA

0.37

0.33

9.90

1.17

DEthreader

DFVDVLHTFTRGIGIQKPVGHVDIYPNGGTFQPGCNIGEA-VDQLVKCSHERSIHLFIDSLLNENPSKAYRCSSKEAFEKGLCLSCR-K--NRCNNLGYEI-NKV--RA------KASSKMYLKTRSQMPYK

2pplA3

0.36

0.33

9.70

3.86

SPARKS-K

DFVDVIHTDAAGFGTNQQMGHLDFFPNGGESMPGCNALSQIVDLFVACNHLRSYKYYLESILNPDGFAAYPCTSYKSFESDKCFPCP---DQGCPQMGHYADKF---------AGREQQKFFLNTGEASNFA

6e7kA

0.37

0.33

9.90

1.53

MapAlign

-FVDVLHTFTRSIGIQKPVGHVDIYPNGGTFQPGCNIGAGDVDQLVKCSHERSIHLFIDSLLNENPSKAYRCSSKEAFEKGLCLSC---RKNRCNNLGYEI--NK--V-----RAKASSKMYLKTRSQMPYK

2pvsB3

0.40

0.37

10.95

1.48

CEthreader

VFVDVIHTDSSGFGMSQKVGHLDFFPNGGKEMPGCKKNIDGIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPCPA---EGCPKMGHYADQFKGKT------SAVEQTFFLNTGESGQFT

2pvsB3

0.38

0.36

10.55

2.46

MUSTER

VFVDVIHTDSSGFGMSQKVGHLDFFPNGGKEMPGCKGIWEGIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPC---PAEGCPKMGHYADQFKGKTSA------VEQTFFLNTGESGQFT

2pplA

0.38

0.34

10.11

4.01

HHsearch

DFVDVIHTDAAGFGTNQQMGHLDFFPNGGESMPGCKKNALSTRDFVACNHLRSYKYYLESILNPDGFAAYPCTSYKSFESDKCFPCPD---QGCPQMGHYADKFA---------GREQQKFFLNTGEASNFA

2pvsB3

0.39

0.36

10.75

1.75

FFAS-3D

VFVDVIHTDSLGFGMSQKVGHLDFFPNGGKEMPGCKKNWEGIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPCPA---EGCPKMGHYADQFKGK------TSAVEQTFFLNTGESGQFT

2pvsB3

0.34

0.31

9.31

1.50

EigenThreader

VFVDVIHTDSLGFGMSQKVGHLDFFPNGGKEMPGCKKIWEGIGGFVSCNHLRSFEYYSSSVLNPDGFLGPCASYDEFQESKCFPCPAEG----CPKMGHYADQFKGKT------SAVEQTFFLNTGESGQFT

1gplA

0.40

0.35

10.29

3.10

CNFpred

KFVDVIHTDISGFGMSQKVGHMDFFPNGGKDMPGCKTGI-------SCNHHRSIEYYHSSILNPEGFLGYPCASYDEFQESGCFPCPA---KGCPKMGHFADQYPGKTN------AVEQTFFLNTGASDNFT

6e7kA1

0.37

0.33

9.90

1.17

DEthreader

DFVDVLHTFTRGIGIQKPVGHVDIYPNGGTFQPGCNIGEA-VDQLVKCSHERSIHLFIDSLLNENPSKAYRCSSKEAFEKGLCLSCR-K--NRCNNLGYEI-NKV--RA------KASSKMYLKTRSQMPYK

(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	0.8154

(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	2pplA3	0.84	1.78	0.375	0.909	model1_2pplA3.pdb.gz
2	2pvsB	0.83	2.05	0.393	0.924	model1_2pvsB.pdb.gz
3	1ethA3	0.82	1.97	0.374	0.909	model1_1ethA3.pdb.gz
4	4qnnA	0.70	1.77	0.295	0.795	model1_4qnnA.pdb.gz
5	1xr2B2	0.42	4.03	0.057	0.674	model1_1xr2B2.pdb.gz
6	5dbjE	0.37	5.66	0.042	0.750	model1_5dbjE.pdb.gz
7	2b39A	0.34	4.81	0.024	0.621	model1_2b39A.pdb.gz
8	3q73A	0.31	4.40	0.024	0.508	model1_3q73A.pdb.gz
9	3e0xA	0.29	5.51	0.044	0.576	model1_3e0xA.pdb.gz
10	2hcrB1	0.28	4.40	0.065	0.455	model1_2hcrB1.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:0016788	0.99	hydrolase activity, acting on ester bonds
GO:0016298	0.98	lipase activity
GO:0052689	0.71	carboxylic ester hydrolase activity
GO:0004806	0.68	triglyceride lipase activity
GO:0004465	0.50	lipoprotein lipase activity

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:0044699	0.77	single-organism process
GO:0008152	0.65	metabolic process
GO:0050896	0.61	response to stimulus
GO:0071704	0.60	organic substance metabolic process
GO:0044710	0.59	single-organism metabolic process
GO:0044238	0.59	primary metabolic process
GO:0042221	0.57	response to chemical
GO:0010033	0.56	response to organic substance
GO:0009987	0.55	cellular process
GO:1901700	0.54	response to oxygen-containing compound
GO:0006629	0.51	lipid metabolic 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:0044421	0.94	extracellular region part
GO:0005615	0.88	extracellular space
GO:0044464	0.85	cell part
GO:0044424	0.75	intracellular part
GO:0043226	0.52	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	3b9xC	0.337	4.79	0.036	0.591	3.2.2.8	NA
2	0.060	3fimB	0.430	4.81	0.043	0.750	1.1.3.7	NA
3	0.060	2qrlA	0.467	4.52	0.053	0.803	1.5.1.7	NA
4	0.060	1bu8A	0.833	2.08	0.390	0.932	3.1.1.3	NA
5	0.060	1rp1A	0.807	1.58	0.383	0.871	3.1.1.3	8

	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	0.18	1lpbB	0.830	1.99	0.374	0.917	0.27	MUP	complex1.pdb.gz	29,74,123
2	0.06	1ethA	0.821	1.97	0.374	0.909	0.27	UUU	complex2.pdb.gz	9,27,28
3	0.01	3qmoB	0.447	4.91	0.067	0.788	0.12	NS4	complex3.pdb.gz	15,34,49,54
4	0.01	3ln1A	0.448	4.92	0.059	0.788	0.14	CEL	complex4.pdb.gz	7,53,56,57,60,61
5	0.01	1cx2A	0.444	4.85	0.050	0.780	0.15	HEM	complex5.pdb.gz	28,35,56,59,63
6	0.01	3pghA	0.445	4.72	0.059	0.773	0.11	FLP	complex6.pdb.gz	9,15,51,55
7	0.01	1pxxC	0.445	4.66	0.059	0.765	0.10	HEM	complex7.pdb.gz	24,26,30,31,52
8	0.01	3mqeA	0.438	4.87	0.067	0.773	0.16	HEM	complex8.pdb.gz	15,19,55
9	0.01	1ddxB	0.447	4.72	0.060	0.765	0.12	PGX	complex9.pdb.gz	17,19,30
10	0.01	3q7dB	0.444	4.78	0.059	0.773	0.13	NPX	complex10.pdb.gz	12,15,34,36

	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.