D-I-TASSER Q06190-D2

D-I-TASSER results for Q06190-D2

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

Input Sequence in FASTA format

>Q06190 (148 residues)
VVHHSVCADLLHIPVSQFKDADLNSMFLPHENGLSSAEGDYPQQAFTGIPRVKRGSTFQN
TYNLKDIAGEAISFASGKIKEFSFEKLKNSNHAAYRKGRKVKSDSFNRRSVDLDLLCEDL
VTQILEKHKIDNFSSGTDIKMCLDILLK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VVHHSVCADLLHIPVSQFKDADLNSMFLPHENGLSSAEGDYPQQAFTGIPRVKRGSTFQNTYNLKDIAGEAISFASGKIKEFSFEKLKNSNHAAYRKGRKVKSDSFNRRSVDLDLLCEDLVTQILEKHKIDNFSSGTDIKMCLDILLK
Prediction	CCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCHHHHHHHHHHHHCCCCHHHCHHHHHCCCHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHC
Confidence	9533566777528865457877675324677886677777762011688777666401133456664677776412542120088751344245652765688755545430889999999999998514678875028899999849
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VVHHSVCADLLHIPVSQFKDADLNSMFLPHENGLSSAEGDYPQQAFTGIPRVKRGSTFQNTYNLKDIAGEAISFASGKIKEFSFEKLKNSNHAAYRKGRKVKSDSFNRRSVDLDLLCEDLVTQILEKHKIDNFSSGTDIKMCLDILLK
Prediction	7433410241251425525547154422346431435656334421443452544432444241451244015234341461326404655333245345145551544413132004400340155252653453530300030138
	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

CCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCHHHHHHHHHHHHCCCCHHHCHHHHHCCCHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHC
VVHHSVCADLLHIPVSQFKDADLNSMFLPHENGLSSAEGDYPQQAFTGIPRVKRGSTFQNTYNLKDIAGEAISFASGKIKEFSFEKLKNSNHAAYRKGRKVKSDSFNRRSVDLDLLCEDLVTQILEKHKIDNFSSGTDIKMCLDILLK

6hr7A1

0.10

3.74

0.56

CEthreader

CVDKKPAGINLIEGRGKSIIAEVFLKEEEIKKYLKTTSKAIEQVNMYKNLIGSAISNSMGFNAHYANIIGALFLATGQDEAHIVEGSLGITVAECTEDGVYFSVTLPDVPVGTGGTRVETQKECLELLGCHGGDKALKFAEIVGATVL

1tj7A

0.10

0.09

3.53

0.57

EigenThreader

DESRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDR----DHVLELLSAAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQGALTGMMMTLKGLFDALDTWLD

2mvgA

0.15

0.09

3.18

0.41

FFAS-3D

---------------------------------------------------LVERTNAALESSSKDLKNKILKIK----KEATGKGVLFEAFTGLKTGSKVTSGGLALREAKVQAITGKFLKIIEEEAKLKETGNSGQFLAMFDLMLE

6y5qq

0.08

0.07

2.99

0.62

SPARKS-K

VEEDRNTNVYVSGLPPDITVDEFIQLMKFGIIMRDPQTEEFKVKLYKDNQGNLKGDGLCCYLK-RESVELALKLLDEDEYKLHVEVAKFQLRVVIIKNM-FHPMDFE-DDPLVLNEIREDLRVECSKFGFDRHPDGRDPEEADYCIQT

3ccyA

0.14

0.07

2.54

0.53

CNFpred

---------------------------------------------------------------RDTIIERAAAMFAQGYSETSIGDIARACECS------RLYHYFDSKEAVLRDMLTTHVDSLLERCRQVSNEPKTRFLQIVKLFLE

4a01A

0.05

0.04

1.93

1.00

DEthreader

VSKIVMGFLLAGLVLYAIFKYGLFEAITGGGYSSCALVVAS-------HELTAMLYPLVSSVGILVCLLTTLFATDFFEIPALKKQLV-I-STVLM---TIGVAWFLCVALWMSTIATGLAIDAYGPISDNTALD--G----------

6hr7A1

0.07

2.82

0.71

MapAlign

DKKPAGINLIEGRGKSIIAEVFLKEEEIKKYLKTTSKAI-EQVNMYKNLIGSAISNSMGFNAHYANIIGALFLATGQDEAHIVEGSLGITVAECTEDGVYFSVTLPDVPVGTVGGGTRETQKECLELLGCHGGKALKFAEIVGATVLA

4qn8A

0.11

0.10

3.65

0.46

MUSTER

--PLTQTQRLINTYGASLKNGTISNIILLDPNTFTKSEGY-----------VDPNAPVSDSNHSKDAIKDFVLTIGPTLDSEILHQLTSRELSPPGDRNTFRGSSLEKAFLAFEAHYPTKAEEHFNSTRVRTEFPGNDIDNLKAVILN

4ic9A

0.21

0.11

3.66

0.53

HHsearch

----------------------------------------------------------GQGRDWKMAIKRCSNVAVGKSKKFGEGNFRWARMANVSTGREPGDIPE-----TLDQ-LRLVICDLQER--REKFGSSKEIDMAIVTLKV

5mrcGG

0.08

0.07

2.89

0.49

CEthreader

AEQLAQWEALKSVPIPPRKNATLDHITMIMRHGKKEKAQTILSRALYLVYC-------QTRQDPIQALEKSLDEL---APLMMTKTFNTGVAKASVIPVPLNKRQ-------RNRIAWNWIVQSANQ-RVSSDFAVRLGEELTAIAKG

(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	0.5266

(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	6btmF	0.48	4.18	0.063	0.730	model1_6btmF.pdb.gz
2	4gbyA	0.48	4.74	0.078	0.770	model1_4gbyA.pdb.gz
3	3w0lB	0.47	4.87	0.068	0.804	model1_3w0lB.pdb.gz
4	6f0kF	0.47	4.67	0.053	0.757	model1_6f0kF.pdb.gz
5	4j05A	0.47	4.48	0.056	0.730	model1_4j05A.pdb.gz
6	6apjA	0.46	4.88	0.050	0.797	model1_6apjA.pdb.gz
7	2xr1A	0.46	5.01	0.070	0.818	model1_2xr1A.pdb.gz
8	6f0kC	0.46	4.82	0.045	0.770	model1_6f0kC.pdb.gz
9	3fr8B	0.46	4.81	0.064	0.797	model1_3fr8B.pdb.gz
10	7crzA	0.46	4.64	0.053	0.730	model1_7crzA.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:0030674	1.00	protein binding, bridging
GO:0008601	1.00	protein phosphatase type 2A regulator 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:0090263	1.00	positive regulation of canonical Wnt signaling pathway
GO:0090249	1.00	regulation of cell motility involved in somitogenic axis elongation
GO:0090244	1.00	Wnt signaling pathway involved in somitogenesis
GO:0061053	1.00	somite development
GO:0007525	1.00	somatic muscle development
GO:0001754	1.00	eye photoreceptor cell differentiation
GO:0080090	0.72	regulation of primary metabolic process
GO:0008152	0.72	metabolic process
GO:0071704	0.71	organic substance metabolic process
GO:0044238	0.71	primary metabolic process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0051246	0.69	regulation of protein metabolic process
GO:0044260	0.69	cellular macromolecule metabolic process
GO:0009893	0.69	positive regulation of metabolic process
GO:0048523	0.68	negative regulation of cellular process
GO:0010604	0.68	positive regulation of macromolecule metabolic process
GO:0051247	0.67	positive regulation of protein metabolic process
GO:0009896	0.67	positive regulation of catabolic process
GO:0006796	0.67	phosphate-containing compound metabolic process
GO:0006464	0.67	cellular protein modification process
GO:0090090	0.66	negative regulation of canonical Wnt signaling pathway
GO:0045732	0.66	positive regulation of protein catabolic process
GO:0006470	0.66	protein dephosphorylation

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:0000159	1.00	protein phosphatase type 2A complex

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	1ah7A	0.438	4.36	0.064	0.703	3.1.4.3	NA
2	0.060	3k9fA	0.451	4.82	0.054	0.730	5.99.1.-	NA
3	0.060	2bpiA	0.433	4.95	0.078	0.763	1.15.1.1	NA
4	0.060	1m0wA	0.445	4.87	0.026	0.757	6.3.2.3	NA
5	0.060	1onkA	0.441	4.69	0.043	0.716	3.2.2.22	70

	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	0.06	1qzfA	0.446	4.53	0.069	0.710	0.20	FOL	complex1.pdb.gz	67,76,79,80,96,100,117
2	0.06	1sejA	0.448	4.50	0.069	0.710	0.12	F89	complex2.pdb.gz	113,114,117
3	0.05	3dl6C	0.450	4.50	0.070	0.710	0.31	DHF	complex3.pdb.gz	68,76,77,99,117
4	0.05	1qzfA	0.446	4.53	0.069	0.710	0.17	NDP	complex4.pdb.gz	68,69,70,118,119,121
5	0.05	1t10A	0.448	4.86	0.052	0.790	0.35	F6P	complex5.pdb.gz	72,99,100,114
6	0.04	3hj3B	0.447	4.50	0.069	0.710	0.21	MTX	complex6.pdb.gz	69,70,98,112,116,117,124
7	0.01	1sejE	0.448	4.50	0.069	0.710	0.19	F89	complex7.pdb.gz	66,70,104
8	0.01	3hj3C	0.448	4.33	0.070	0.696	0.19	MTX	complex8.pdb.gz	67,68,69,102,109
9	0.01	3ujhA	0.448	5.24	0.029	0.818	0.12	G6Q	complex9.pdb.gz	67,69,70
10	0.01	3hj3C	0.448	4.33	0.070	0.696	0.17	NDP	complex10.pdb.gz	70,86,87

	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.