D-I-TASSER Q02535-D1

D-I-TASSER results for Q02535-D1

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

Input Sequence in FASTA format

>Q02535 (119 residues)
MKALSPVRGCYEAVCCLSERSLAIARGRGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPR
GTQLSQVEILQRVIDYILDLQVVLAEPAPGPPDGPHLPIQTAELTPELVISNDKRSFCH

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MKALSPVRGCYEAVCCLSERSLAIARGRGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQVVLAEPAPGPPDGPHLPIQTAELTPELVISNDKRSFCH
Prediction	CCCCCCCCCCCCCCCCHCHHCHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCC
Confidence	98755667753232011110100025666665201257788788999999999668999988511999999999999999999844787777888889876666720001588763459
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MKALSPVRGCYEAVCCLSERSLAIARGRGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQVVLAEPAPGPPDGPHLPIQTAELTPELVISNDKRSFCH
Prediction	75334424524522222364344135444545447443323441540143046114513774524314103201410230331054555556744544264443334333477644317
	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

CCCCCCCCCCCCCCCCHCHHCHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCC
MKALSPVRGCYEAVCCLSERSLAIARGRGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQVVLAEPAPGPPDGPHLPIQTAELTPELVISNDKRSFCH

4ayaA

0.52

0.25

7.29

1.02

FFAS-3D

----------------------------------DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHLKPSF---------------------------

4ayaA

0.51

0.25

7.30

1.25

MUSTER

----------------------------------DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHLKPSFL--------------------------

4ayaA

0.51

0.25

7.30

2.45

HHsearch

----------------------------------DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHLKPSFL--------------------------

6gmmA

0.10

3.72

0.56

CEthreader

ISPCGPGKDTSKNGGVQTFTITCGTTGYEPGPYSILSTENYAKINKAYQIIQKAFGSSGKDIPALSDNNAQVLLEQASTIITTLNSACPWINNGGAGGASSGSLWEGIYLKGDGSACGI

2an0A

0.03

1.64

0.50

EigenThreader

RPSPPEEKGEKQVEIWNHQLIRYAGYEGEAIGD--PASRSLTAACEQLKKVASVIGISTNYNTDLWK---DQALVELNKAVLYSYKKQGVSEQEEEAGRKLTGDWTWLIPPISGAATHI

2ypaA

0.23

0.13

3.95

0.99

FFAS-3D

------------------------TKVVRRIFTNSRERWRQQNVNGAFAELRKLIPTHPPDKKLSKNEILRLAMKYINFLAKLLNDQEE------------------------------

4ayaA

0.51

0.25

7.30

0.95

SPARKS-K

----------------------------------DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHLKPSFL--------------------------

4ayaA

0.58

0.25

7.24

0.59

CNFpred

----------------------------------DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDS---------------------------------

4cvuA

0.05

0.04

1.99

0.83

DEthreader

TGKSQAHL-ESNNNQAVEFNSTTVI------GLTRN-IHNSTLGQVEMTLAVERYY-PTPDKNSSWCHATQLFQADMYKSEIQFYRSFEIALFLPVPALY--TWL--THPAG-L---TE

5iv5L

0.09

3.50

0.89

MapAlign

RLADFLGFRPKTGDIDVMNRQSVGSVTISQFYEPNIESAINDVHNFSFSGTVLVFLPVSATTGMTAIEFVAKVRVALQEAIANSYKDHPTDGSKLEVTYLDNQKHVLSTYSTYGITISQ

(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	0.5242

(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	5jtaA	0.52	4.25	0.073	0.849	model1_5jtaA.pdb.gz
2	5d06A	0.49	4.40	0.094	0.840	model1_5d06A.pdb.gz
3	5xguB	0.49	3.95	0.063	0.765	model1_5xguB.pdb.gz
4	3mk7A	0.48	3.82	0.057	0.740	model1_3mk7A.pdb.gz
5	1y2mB	0.48	4.67	0.071	0.857	model1_1y2mB.pdb.gz
6	5jcss	0.48	4.81	0.056	0.874	model1_5jcss.pdb.gz
7	3rfuA	0.48	4.85	0.095	0.857	model1_3rfuA.pdb.gz
8	6p25A	0.47	4.67	0.053	0.807	model1_6p25A.pdb.gz
9	6f3hA2	0.47	4.36	0.055	0.790	model1_6f3hA2.pdb.gz
10	7jroa	0.47	4.14	0.094	0.781	model1_7jroa.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:0008134	0.62	transcription factor 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:0065007	0.97	biological regulation
GO:0050789	0.97	regulation of biological process
GO:0050794	0.96	regulation of cellular process
GO:0048523	0.91	negative regulation of cellular process
GO:0060255	0.89	regulation of macromolecule metabolic process
GO:0010468	0.88	regulation of gene expression
GO:0080090	0.83	regulation of primary metabolic process
GO:0031323	0.83	regulation of cellular metabolic process
GO:0006355	0.82	regulation of transcription, DNA-templated
GO:0044699	0.79	single-organism process
GO:0045892	0.77	negative regulation of transcription, DNA-templated
GO:0009987	0.77	cellular process
GO:0044763	0.69	single-organism cellular process
GO:0032502	0.68	developmental process
GO:0044767	0.67	single-organism developmental process
GO:0048869	0.63	cellular developmental process
GO:0045595	0.58	regulation of cell differentiation
GO:0009653	0.55	anatomical structure morphogenesis
GO:0048518	0.54	positive regulation of biological process
GO:0045596	0.54	negative regulation of cell differentiation
GO:0051239	0.53	regulation of multicellular organismal process
GO:0050793	0.53	regulation of developmental process
GO:0050896	0.51	response to stimulus
GO:0048856	0.51	anatomical structure development

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:0043229	0.85	intracellular organelle
GO:0043231	0.81	intracellular membrane-bounded organelle
GO:0005634	0.80	nucleus
GO:0044422	0.63	organelle part
GO:0044446	0.62	intracellular organelle part
GO:0032991	0.56	macromolecular complex
GO:0043234	0.53	protein complex
GO:0044428	0.52	nuclear part

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	2ebaA	0.454	4.63	0.065	0.740	1.3.99.7	NA
2	0.060	1hwnA	0.442	3.72	0.038	0.655	3.2.2.22	50
3	0.060	1pumA	0.451	3.73	0.050	0.681	3.2.2.22	NA
4	0.060	1hcuB	0.446	4.71	0.028	0.756	3.2.1.113	NA
5	0.060	2oqaA	0.436	3.86	0.000	0.681	3.2.2.22	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	3rkoC	0.458	4.91	0.068	0.807	0.23	CA7	complex1.pdb.gz	45,52,62
2	0.01	3ag4A	0.470	4.87	0.061	0.891	0.24	CDL	complex2.pdb.gz	44,48,51,55
3	0.01	1v54A	0.469	4.93	0.069	0.899	0.20	CDL	complex3.pdb.gz	51,55,61
4	0.01	1oczN	0.464	4.84	0.035	0.866	0.11	HEA	complex4.pdb.gz	41,47,57,59,69,70,73
5	0.01	1v54A	0.469	4.93	0.069	0.899	0.10	HEA	complex5.pdb.gz	58,59,62,64,70,73,115
6	0.01	1ocoA	0.465	4.84	0.053	0.866	0.11	UUU	complex6.pdb.gz	4,46,56,57,58,65,115
7	0.01	1fftA	0.457	4.73	0.028	0.807	0.10	HEM	complex7.pdb.gz	55,60,74
8	0.01	2eijN	0.469	5.00	0.052	0.908	0.10	HEA	complex8.pdb.gz	57,58,60,65,70,73
9	0.01	1fftA	0.457	4.73	0.028	0.807	0.11	HEO	complex9.pdb.gz	49,58,62,74
10	0.01	2ptrA	0.458	4.40	0.088	0.781	0.21	2SA	complex10.pdb.gz	58,59,60,61

	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.