D-I-TASSER Q13127-D4

D-I-TASSER results for Q13127-D4

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

Input Sequence in FASTA format

>Q13127 (60 residues)
VPKGDSKVEENKKQNTCMKKSTKKKTLKNKSSKKSSKPPQKEPVEKGSAQMDPPQMGPAP

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| VPKGDSKVEENKKQNTCMKKSTKKKTLKNKSSKKSSKPPQKEPVEKGSAQMDPPQMGPAP
Prediction	CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	998742356643332677654456654134444468876668887776556898788899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| VPKGDSKVEENKKQNTCMKKSTKKKTLKNKSSKKSSKPPQKEPVEKGSAQMDPPQMGPAP
Prediction	866566535655554433455355542555646666544675447656463545636658
	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

                   |                   |                   |

SS
Seq

CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
VPKGDSKVEENKKQNTCMKKSTKKKTLKNKSSKKSSKPPQKEPVEKGSAQMDPPQMGPAP

5n6xA

0.04

0.03

1.82

1.17

DEthreader

KKPIEANLQMAEKSKAGLEEKLSGLKTRLPSCIERFFMQIEIND-I-KTLIR--YVYVY-

2zagD1

0.05

2.35

0.57

CEthreader

PLPRYGEKYVNLYAKVIVDVSNSSVKVTVGDRECDPLVTFTPSGKTIKGTGTCSDGNAFP

6co7A3

0.07

2.80

0.50

EigenThreader

FIAHTSCQVLLTRLWMGTMAMNTMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFD

2xd8A2

0.13

0.12

4.07

0.24

FFAS-3D

VSSQGRCAVLNPRQYYALIQDIGSNGLVNRDVQGSALQSGNGVIEIAGIHIYKSM-----

5lqxI

0.15

0.13

4.52

0.99

SPARKS-K

WQKAGISFNKYLAIAARTVQRSLKNDLKVAAEKRYISDAKVQKLEKVSTTDLASN-----

3j39R

0.08

0.05

1.98

0.96

CNFpred

----------------------RSKMLADQAEARRQKVREARKRREERIATKKQELIALH

6tdxG

0.07

2.75

1.00

DEthreader

GGGTIRFWREKLEGYKKYHQIVKTIKMV-LAKYRQTVRRDQTLRY--TRKLDATQDVIEK

2zagD1

0.05

2.35

0.82

MapAlign

PLPRYGEKYVNLYAKVIVDVSNSSVKVTVGDRECDPLVTFTPSGKTIKGTGTCSDGNAFP

2kk9A

0.17

0.15

4.95

0.88

MUSTER

--KGLRRLDASREAKKQLEAEQQKLEEQNKISEASRKGLRRDLDASREAKKQVEKA----

1svbA

0.18

5.95

0.41

HHsearch

YDANKIVVEPHTDQTGVLLKAGTKYHLKEKLKKGLTYTMCDKTWKRAPTDSGHDTVGTKP

(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	0.3923

(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	5gufA	0.48	3.85	0.017	0.867	model1_5gufA.pdb.gz
2	5eikA	0.48	3.82	0.051	0.967	model1_5eikA.pdb.gz
3	3no6A	0.47	3.45	0.071	0.800	model1_3no6A.pdb.gz
4	2yiuB	0.47	3.32	0.020	0.833	model1_2yiuB.pdb.gz
5	6wlfA	0.47	3.19	0.125	0.800	model1_6wlfA.pdb.gz
6	1awzA	0.47	3.79	0.034	0.883	model1_1awzA.pdb.gz
7	3ce9A	0.46	4.16	0.034	0.850	model1_3ce9A.pdb.gz
8	2gm8A	0.46	3.69	0.085	0.850	model1_2gm8A.pdb.gz
9	3mvuA	0.45	3.63	0.069	0.850	model1_3mvuA.pdb.gz
10	1kq3A	0.45	3.56	0.035	0.783	model1_1kq3A.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:0000981	1.00	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0097159	0.66	organic cyclic compound binding
GO:1901363	0.65	heterocyclic compound binding
GO:0003676	0.56	nucleic acid binding
GO:0003677	0.53	DNA binding
GO:0003682	0.51	chromatin binding
GO:0044212	0.50	transcription regulatory region DNA 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:2000798	1.00	negative regulation of amniotic stem cell differentiation
GO:2000706	1.00	negative regulation of dense core granule biogenesis
GO:2000065	1.00	negative regulation of cortisol biosynthetic process
GO:0071385	1.00	cellular response to glucocorticoid stimulus
GO:0071257	1.00	cellular response to electrical stimulus
GO:0070933	1.00	histone H4 deacetylation
GO:0060379	1.00	cardiac muscle cell myoblast differentiation
GO:0046676	1.00	negative regulation of insulin secretion
GO:0045955	1.00	negative regulation of calcium ion-dependent exocytosis
GO:0045892	1.00	negative regulation of transcription, DNA-templated
GO:0045665	1.00	negative regulation of neuron differentiation
GO:0043922	1.00	negative regulation by host of viral transcription
GO:0043280	1.00	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0035690	1.00	cellular response to drug
GO:0032348	1.00	negative regulation of aldosterone biosynthetic process
GO:0008285	1.00	negative regulation of cell proliferation

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:0005634	1.00	nucleus
GO:0032991	0.58	macromolecular complex
GO:0043234	0.57	protein 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	1a4yB	0.480	3.91	0.052	0.917	3.1.27.-	NA
2	0.060	3cxhO	0.439	3.53	0.039	0.850	1.10.2.2	NA
3	0.060	2g2dA	0.442	3.47	0.000	0.817	2.5.1.17	NA
4	0.060	2g8sA	0.372	3.78	0.082	0.783	1.1.5.-	NA
5	0.060	2j6xH	0.381	3.95	0.058	0.833	1.1.3.2	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	0.01	1t76A	0.439	3.62	0.018	0.833	0.26	III	complex1.pdb.gz	4,11,54
2	0.01	2nw4A	0.444	3.93	0.036	0.883	0.15	8NH	complex2.pdb.gz	4,7,8,10,11,14
3	0.01	2vbfA	0.343	4.48	0.074	0.817	0.21	TPP	complex3.pdb.gz	37,38,39,45,46
4	0.01	1xj7A	0.438	3.83	0.018	0.867	0.13	III	complex4.pdb.gz	6,9,13
5	0.01	2yiuE	0.469	3.38	0.020	0.833	0.13	HEC	complex5.pdb.gz	49,50,51,54
6	0.01	1t73A	0.441	4.06	0.034	0.900	0.17	III	complex6.pdb.gz	5,8,12
7	0.01	1t79A	0.365	3.52	0.037	0.733	0.21	III	complex7.pdb.gz	4,7,11,44
8	0.01	1e3gA	0.443	3.78	0.018	0.867	0.12	R18	complex8.pdb.gz	7,8,14
9	0.01	1i37A	0.375	3.81	0.056	0.817	0.11	DHT	complex9.pdb.gz	4,5,7,8,11
10	0.01	1a4y4	0.480	3.91	0.052	0.917	0.16	III	complex10.pdb.gz	7,10,14

	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.