D-I-TASSER Q9P2M1-D3

D-I-TASSER results for Q9P2M1-D3

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

Input Sequence in FASTA format

>Q9P2M1 (122 residues)
DTEAALQCLREAAERGNVYAQGNLVEYYYKMKFFTKCVAFSKRIADYDEVHDIPMIAQVT
DCLPEFIGRGMAMASFYHARCLQLGLGITRDETTAKHYYSKACRLNPALADELHSLLIRQ
RI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| DTEAALQCLREAAERGNVYAQGNLVEYYYKMKFFTKCVAFSKRIADYDEVHDIPMIAQVTDCLPEFIGRGMAMASFYHARCLQLGLGITRDETTAKHYYSKACRLNPALADELHSLLIRQRI
Prediction	CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCC
Confidence	86899999999999187889999999999802379999999888721332235889999973699999824789999999999289987689999999999998098999999999972569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| DTEAALQCLREAAERGNVYAQGNLVEYYYKMKFFTKCVAFSKRIADYDEVHDIPMIAQVTDCLPEFIGRGMAMASFYHARCLQLGLGITRDETTAKHYYSKACRLNPALADELHSLLIRQRI
Prediction	85740251045127433330322002102444214400630442063544552641453251245114402020232102025334335534740451043027344510440343144657
	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 DeepPotential. 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

CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCC
DTEAALQCLREAAERGNVYAQGNLVEYYYKMKFFTKCVAFSKRIADYDEVHDIPMIAQVTDCLPEFIGRGMAMASFYHARCLQLGLGITRDETTAKHYYSKACRLNPALADELHSLLIRQRI

6c95A

0.10

0.09

3.36

1.17

DEthreader

QPSIALEYINTAIETTLIELFLVKAKIYKHAGNIKEAARWMDEAQALDTADRFINSKCAKYMLIECAVNLCMWFQTECAQAYK-A-----MNK-FGEALKKCHE-IEYKAARIAIEIYLKL-

5b26A

0.17

0.16

5.40

1.24

SPARKS-K

LEEDLIQYYQFLAEKGDVQAQVGLGQLHLHGGNHQRAFDYFNLAANAG---NSHAMAFLGKMYSKAADMGNPVGQSGLGMAYLYGRGVQVNYDLALKYFQKAAEQWVDGQLQLGSMYYNGIG

2xm6A2

0.21

0.18

5.72

1.67

FFAS-3D

EHKKAVEWFRKAAAKGEKAAQFNLGNALLQGKGVKKDEQ------------------QAAIWMRKAAEQGLSAAQVQLGEIYYYGLGVERDYVQAWAWFDTASTNDMNLFGTENRNITEKKL

5nnpA

0.13

0.12

4.25

1.17

DEthreader

DLTRALEYVEKAIEPKNVDFHMTKARIFKHQGDLAKAAETMDYARSLDPKDRY-INSKAAKQLNLMPLDLCIWFLTEDGEAWQ------RRGN--TALALKRYHTVFYRAALDAVNLYLSMK

6dehA

0.21

0.20

6.51

1.18

SPARKS-K

DKTQALNWYAKAADLGNASAQYNLGLMYEQGKDYQKAAEYFEKAANQG---HAKSQLELGYLYDSSADLGNANAQFNLADMYFYGDGVGKSLEQSVYWMQKAAEQYGKAQNQLGIYYRDGIG

1ouvA

0.21

0.20

6.50

0.66

MapAlign

-TNKALQYYSKACDLKYAEGCASLGGIYHDVRDFKKAVEYFTKACDL---NDGDGCTILGSLYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELNGGGCFNLGAMQYNGEG

6dehA

0.21

0.20

6.51

0.46

CEthreader

DKTQALNWYAKAADLGNASAQYNLGLMYEQPKDYQKAAEYFEKAANQG---HAKSQLELGYLYDSGKLGGNANAQFNLADMYFYGDGVGKSLEQSVYWMQKAAEQYGKAQNQLGIYYRDGIG

6dehA

0.22

6.98

0.95

MUSTER

DKTQALNWYAKAADLGNASAQYNLGLMYEQGKDYQKAAEYFEKAANQGHAKSKSDLQKAAFWYQKSADLGNANAQFNLADMYFYGDGVGKSLEQSVYWMQKAAEQGYGKAQNQLGIYYRDGI

3pe3A

0.16

5.16

0.60

HHsearch

NIEEAVRLYRKALFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGNTYTRAINPAFADAHSNLASIHKDS----GNIPEAIASYRTALKLFPDAYCNLAHCLQICDW

6ur7A

0.22

0.21

6.74

1.63

FFAS-3D

NAEIANQWYLKAAEQGFAKAQFNLGLSYEKGTGISKNMVEAVKWYRKQGNGVKKDPNRAVQYYIMGAEKGDGEAQLFLADCYAKASGIPYDADRALYWYKESAKNGNITAMKVLSGIYKQ--

(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	0.6497

(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 DeepPotential, 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	4kvmA	0.73	2.68	0.078	0.951	model1_4kvmA.pdb.gz
2	5nnpA	0.73	2.71	0.103	0.959	model1_5nnpA.pdb.gz
3	4hnwA	0.72	3.09	0.058	0.984	model1_4hnwA.pdb.gz
4	6c95A	0.72	2.84	0.103	0.959	model1_6c95A.pdb.gz
5	4xdnA	0.71	2.76	0.085	0.967	model1_4xdnA.pdb.gz
6	3e4bC	0.71	2.77	0.196	0.918	model1_3e4bC.pdb.gz
7	1w3bA	0.67	3.14	0.124	0.918	model1_1w3bA.pdb.gz
8	3pe3A1	0.59	2.73	0.110	0.770	model1_3pe3A1.pdb.gz
9	4k92A	0.57	4.25	0.043	0.926	model1_4k92A.pdb.gz
10	4houA	0.56	3.96	0.046	0.844	model1_4houA.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:0036094	0.63	small molecule binding
GO:0003824	0.60	catalytic activity
GO:0016740	0.54	transferase activity
GO:0098772	0.50	molecular function regulator

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	0.86	cellular process
GO:0065007	0.77	biological regulation
GO:0008152	0.75	metabolic process
GO:0071704	0.74	organic substance metabolic process
GO:0050789	0.74	regulation of biological process
GO:0050794	0.73	regulation of cellular process
GO:0044238	0.73	primary metabolic process
GO:0044237	0.73	cellular metabolic process
GO:0043170	0.73	macromolecule metabolic process
GO:0044699	0.71	single-organism process
GO:0044260	0.69	cellular macromolecule metabolic process
GO:0044763	0.67	single-organism cellular process
GO:0019538	0.67	protein metabolic process
GO:0051179	0.62	localization
GO:0019222	0.60	regulation of metabolic process
GO:0050896	0.59	response to stimulus
GO:0044710	0.59	single-organism metabolic process
GO:0044267	0.59	cellular protein metabolic process
GO:0043412	0.59	macromolecule modification
GO:1901575	0.58	organic substance catabolic process
GO:0080090	0.58	regulation of primary metabolic process
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0006464	0.58	cellular protein modification process
GO:0051641	0.57	cellular localization
GO:0032502	0.56	developmental process
GO:0007165	0.56	signal transduction
GO:0051716	0.55	cellular response to stimulus
GO:0051246	0.55	regulation of protein metabolic process
GO:0048519	0.55	negative regulation of biological process
GO:0044767	0.55	single-organism developmental process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0048583	0.54	regulation of response to stimulus
GO:0048523	0.54	negative regulation of cellular process
GO:0042221	0.54	response to chemical
GO:0016043	0.54	cellular component organization
GO:0048518	0.53	positive regulation of biological process
GO:0010033	0.53	response to organic substance
GO:0007166	0.53	cell surface receptor signaling pathway
GO:0006807	0.53	nitrogen compound metabolic process
GO:0048522	0.52	positive regulation of cellular process
GO:0044723	0.52	single-organism carbohydrate metabolic process
GO:0022607	0.52	cellular component assembly
GO:0016310	0.52	phosphorylation
GO:0010941	0.52	regulation of cell death
GO:0009966	0.52	regulation of signal transduction
GO:1901564	0.51	organonitrogen compound metabolic process
GO:0051128	0.51	regulation of cellular component organization
GO:0048856	0.51	anatomical structure development
GO:0048585	0.51	negative regulation of response to stimulus
GO:0044712	0.51	single-organism catabolic process
GO:0032268	0.51	regulation of cellular protein metabolic process
GO:0031326	0.51	regulation of cellular biosynthetic process
GO:0030162	0.51	regulation of proteolysis
GO:0006996	0.51	organelle organization
GO:2000112	0.50	regulation of cellular macromolecule biosynthetic process
GO:1901071	0.50	glucosamine-containing compound metabolic process
GO:0051171	0.50	regulation of nitrogen compound metabolic process
GO:0034641	0.50	cellular nitrogen compound metabolic process
GO:0031399	0.50	regulation of protein modification 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:0044424	1.00	intracellular part
GO:0005737	0.92	cytoplasm
GO:0044444	0.53	cytoplasmic 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	2fbnA	0.561	3.54	0.081	0.853	5.2.1.8	NA
2	0.060	2c0lA	0.694	2.94	0.086	0.951	2.3.1.176	19,23,24,39,43
3	0.060	1z1wA	0.520	4.36	0.079	0.926	3.4.11.-	NA
4	0.060	1nxcA	0.571	4.23	0.078	0.951	3.2.1.113	NA
5	0.060	3dsxA	0.496	4.32	0.053	0.836	2.5.1.60	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.08	3kd7B	0.505	2.93	0.129	0.689	0.75	III	complex1.pdb.gz	19,22,23,26,30

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.