D-I-TASSER Q99627-D2

D-I-TASSER results for Q99627-D2

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

Input Sequence in FASTA format

>Q99627 (125 residues)
DFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPVEEA
VKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFIPLSEPAPVPPIPNEQQLARLTDYV
AFLEN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| DFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFIPLSEPAPVPPIPNEQQLARLTDYVAFLEN
Prediction	CHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCSSCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
Confidence	85899999841899888999999999999999999999986425899999996999999999999829878388875732687765421111011222344556678889999999999997429
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| DFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFIPLSEPAPVPPIPNEQQLARLTDYVAFLEN
Prediction	83640152057360374035005403641253005101410440427302421614473026203734052256442031343455665454554454654443654445620440151033258
	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

CHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCSSCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
DFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFIPLSEPAPVPPIPNEQQLARLTDYVAFLEN

1p4xA

0.07

0.06

2.36

1.00

DEthreader

KYIIIEAYMFFKIKICYMTMYFKNISFFTILAIITSQ-NKNI-VLLKDLIETIHHKYPQTVRALNNLLIKERSERKILIHMDQQDHAEQLLAQVNQLLADKDHHLVFE-----------------

4d10H

0.97

0.77

21.53

1.36

SPARKS-K

DFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPEQQ--------------------------LARLTDYVAFLEN

5l4kS

0.10

0.09

3.29

0.63

MapAlign

NLAKFNQVLDQFGFQDGTYTLIIRLRHNVIKTGVRMISLSYSRISLADIAQKLQLDPEDAEFIVAKIEASINHEKGYVQSKEMIDIYSTREPQ----------LAFHQRISFCLDIHNMSVKAM-

4d10H

1.00

0.79

22.18

0.56

CEthreader

DFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKP--------------------------EQQLARLTDYVAFLEN

4d10H

1.00

0.79

22.18

1.01

MUSTER

DFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKP--------------------------EQQLARLTDYVAFLEN

4d10H

1.00

0.79

22.18

2.45

HHsearch

DFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKP--------------------------EQQLARLTDYVAFLEN

4d10H

0.98

0.78

21.74

1.54

FFAS-3D

DFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPEQ--------------------------QLARLTDYVAFLEN

5mpbP2

0.10

3.52

0.85

EigenThreader

RWPIVQKTYEPVLNEDDLAHHWEDLQKRVIEHNLRVISEYYITL--LRLNELLDLTESQTETYISDLYAKVNRPAKIVNFEKPKNSSQLLNEWSHNVDELLEHIETIGHLITKEEIMH-------

4d10H

1.00

0.79

22.18

1.17

CNFpred

DFPGIYTTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKP--------------------------EQQLARLTDYVAFLEN

4b8xA

0.04

0.03

1.70

1.00

DEthreader

-----------ITIMRAQQILLGEVDTFARYEALVLLTFSKSELPMSKIGERLMVHPTSVTNTVDRLLVAKRPNPGTLATITDKREVVEAATRDLMAMDGLGAYD---------IFAMLRPLRVA

(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	0.6686

(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	4d10H	0.58	1.76	0.828	0.664	model1_4d10H.pdb.gz
2	4cr2T	0.54	2.48	0.133	0.672	model1_4cr2T.pdb.gz
3	4r6iA	0.54	3.25	0.052	0.760	model1_4r6iA.pdb.gz
4	6fec1	0.54	2.69	0.115	0.720	model1_6fec1.pdb.gz
5	4d10C	0.53	2.51	0.083	0.664	model1_4d10C.pdb.gz
6	4b0zA	0.51	2.33	0.167	0.624	model1_4b0zA.pdb.gz
7	3jckA	0.48	3.03	0.070	0.648	model1_3jckA.pdb.gz
8	3sqnA1	0.48	3.70	0.063	0.672	model1_3sqnA1.pdb.gz
9	4d0pA	0.46	3.59	0.148	0.624	model1_4d0pA.pdb.gz
10	4b4tS	0.44	3.45	0.110	0.656	model1_4b4tS.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	0.46	catalytic activity
GO:0016787	0.36	hydrolase activity
GO:0070011	0.34	peptidase activity, acting on L-amino acid peptides
GO:1901363	0.33	heterocyclic compound binding
GO:0097159	0.33	organic cyclic 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:0044260	0.94	cellular macromolecule metabolic process
GO:0044238	0.94	primary metabolic process
GO:0070647	0.93	protein modification by small protein conjugation or removal
GO:0006508	0.93	proteolysis
GO:0010388	0.92	cullin deneddylation
GO:0050794	0.87	regulation of cellular process
GO:0080090	0.84	regulation of primary metabolic process
GO:0060255	0.84	regulation of macromolecule metabolic process
GO:0031323	0.84	regulation of cellular metabolic process
GO:0032268	0.83	regulation of cellular protein metabolic process
GO:0048523	0.82	negative regulation of cellular process
GO:0031399	0.82	regulation of protein modification process
GO:0048522	0.76	positive regulation of cellular process
GO:0050790	0.74	regulation of catalytic activity
GO:0048583	0.74	regulation of response to stimulus
GO:0032270	0.74	positive regulation of cellular protein metabolic process
GO:1902533	0.73	positive regulation of intracellular signal transduction
GO:0051347	0.73	positive regulation of transferase activity
GO:0001934	0.73	positive regulation of protein phosphorylation
GO:0008285	0.72	negative regulation of cell proliferation
GO:0007250	0.72	activation of NF-kappaB-inducing kinase activity
GO:0050896	0.60	response to stimulus
GO:0016043	0.60	cellular component organization

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:0044428	0.95	nuclear part
GO:0005654	0.84	nucleoplasm
GO:0005737	0.83	cytoplasm
GO:0032991	0.72	macromolecular complex
GO:0043234	0.69	protein complex
GO:0043226	0.63	organelle
GO:0043229	0.61	intracellular organelle
GO:0043227	0.61	membrane-bounded organelle
GO:0008180	0.61	COP9 signalosome
GO:0044444	0.60	cytoplasmic part
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0005634	0.57	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	0.060	3bkkA	0.466	4.42	0.080	0.744	3.4.15.1	NA
2	0.060	2q80A	0.490	4.24	0.058	0.792	2.5.1.29 2.5.1.10 2.5.1.1	32
3	0.060	3e7eA	0.469	4.36	0.059	0.776	2.7.11.1	NA
4	0.060	1zcjA	0.487	4.77	0.054	0.848	1.1.1.35	NA
5	0.060	2dh4A	0.509	4.22	0.105	0.816	2.5.1.29	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	0.02	2e8wA	0.509	4.22	0.105	0.816	0.22	IPE	complex1.pdb.gz	29,33,37
2	0.01	1mjbA	0.518	3.94	0.039	0.768	0.15	ACO	complex2.pdb.gz	30,31,32,34,35,62,63
3	0.01	3to7A	0.516	3.96	0.049	0.768	0.15	COA	complex3.pdb.gz	30,31,33,34,58,61,64,91
4	0.01	3n1vF	0.492	4.43	0.049	0.800	0.13	3N1	complex4.pdb.gz	6,29,30
5	0.01	2e94A	0.406	4.96	0.010	0.696	0.12	364	complex5.pdb.gz	54,66,67
6	0.01	2e8uB	0.502	4.12	0.080	0.792	0.22	IPE	complex6.pdb.gz	30,33,37
7	0.01	2vf6A	0.491	4.34	0.039	0.800	0.21	M0N	complex7.pdb.gz	49,50,53,64,67
8	0.01	1zw5A	0.500	4.36	0.038	0.816	0.30	IPR	complex8.pdb.gz	32,50,53,59,60,62
9	0.01	2z78A	0.494	4.07	0.089	0.792	0.13	H86	complex9.pdb.gz	5,32,36,39,40
10	0.01	2e8tA	0.463	3.88	0.071	0.704	0.12	FPS	complex10.pdb.gz	49,53,64,67

	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.