D-I-TASSER Q92900-D2

D-I-TASSER results for Q92900-D2

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

Input Sequence in FASTA format

>Q92900 (107 residues)
KGKTGRGGRQKNRFGLPGPSQTNLPNSQASQDVASQPFSQGALTQGYISMSQPSQMSQPG
LSQPELSQDSYLGDEFKSQIDVALSQDSTYQGERAYQHGGVTGLSQY

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| KGKTGRGGRQKNRFGLPGPSQTNLPNSQASQDVASQPFSQGALTQGYISMSQPSQMSQPGLSQPELSQDSYLGDEFKSQIDVALSQDSTYQGERAYQHGGVTGLSQY
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Confidence	98777786566765688865456766666788767877778666788666788777877777765662101123432345554214443357533335777887889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| KGKTGRGGRQKNRFGLPGPSQTNLPNSQASQDVASQPFSQGALTQGYISMSQPSQMSQPGLSQPELSQDSYLGDEFKSQIDVALSQDSTYQGERAYQHGGVTGLSQY
Prediction	85655645556654445444445454554556444442444424554452454442554425445144443327604442431134424253455254444553566
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
KGKTGRGGRQKNRFGLPGPSQTNLPNSQASQDVASQPFSQGALTQGYISMSQPSQMSQPGLSQPELSQDSYLGDEFKSQIDVALSQDSTYQGERAYQHGGVTGLSQY

3iz5U

0.11

4.03

0.46

CEthreader

RDLFARPFRKKGYIPLTTYLRTYKVGEHVDHGRTGRVWNVTKRAIGVEINKQVRIIKKRIHVRVEHVQPSRCNEEFLQRKLNNDKLKAEAKARGEVISTKRQPAGPK

2yevA2

0.07

2.77

0.53

EigenThreader

LFAILIAGYLYLRLSGAATPPEERPALWLALLNTFLLVSSSFTVHFAHHDLRRGRFNPFRFGLLVTIILGVLFFLGGFGLILAYLQALRGKIHGTLEAASMYWHLVD

2cseW

0.11

0.10

3.68

0.31

FFAS-3D

---------RKTKGKSPATTEPGTSNREQYRARPGIASVQRATESAELPMKNEGTPDKKGNTRGDLVNEHSEAKDEADEATQKQAKDTDKSKAQVYSDTGINNANE-

7jjvA

0.13

4.50

1.28

SPARKS-K

DGLDGADGTSNGQAGASGLAGGPNCN--GGKGGKGAPGVGTAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAA-GGAAGGAGTGGTGGNGGAGKPGGAPGAG

5agdA

0.32

0.07

1.97

0.27

CNFpred

----------------------------------------------------------------QHTSDPALKAELKTQIDDVYDG---------------------

5mrcOO

0.01

1.05

0.83

DEthreader

---------SAKVKFLQRRKNEAKQATLK-AST-DKVD-----PVLGRA---F-EFEAACMTIQNMAIKEHNTRNLRILVQQRQAILRYLKYYWILNDAITD--EFN

4i6hA

0.06

0.05

2.07

0.79

MapAlign

--------------------RIIVDPTTGKRYSRGKTLGKGGFAKCYEMTDLTNNKVYAAKIIPHSRVSKPHQREKIDKEIELHRILHHKHVVQFYHYFEDKENIYI

2nbiA2

0.09

0.08

3.23

0.71

MUSTER

QPSSQPTGPQPSSQPSECADVLELCPYDTCFLPFDDSSRPPDCTDPSVNRPDCDKLSTADFTCPTCCPTQCRPD----NPMFSPSPDGSPPVCSPTMMPSPLPSPTE

4f91B3

0.13

4.53

0.50

HHsearch

SDDPTGSGKTICATGETSGNIISTPEKFVVDHLIGGELSPVPLELPVISRKTLKELNGVGYLHEGLSPMELVEQLFSSGAIQVVVSRSLCWGHLVIIMDTHANRPLQ

4lqeA

0.07

2.72

0.46

CEthreader

----MYKSKILLKYIFSEESEVKDLTETFSFKEETYQSKEAFADYLMIIVIDEELSGYFLFPRELLVEKGILTTFEHKGKMAFRVYPKWNQLNKTAG-QTQKWQCKY

(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	0.4637

(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	3owaA	0.49	3.94	0.032	0.794	model1_3owaA.pdb.gz
2	1ivhA	0.49	3.96	0.065	0.804	model1_1ivhA.pdb.gz
3	6es9A	0.49	3.94	0.042	0.804	model1_6es9A.pdb.gz
4	2jifA	0.49	4.09	0.065	0.804	model1_2jifA.pdb.gz
5	2d29A	0.49	3.86	0.056	0.785	model1_2d29A.pdb.gz
6	1jkyA	0.48	3.94	0.063	0.766	model1_1jkyA.pdb.gz
7	4zxvA	0.48	4.18	0.052	0.832	model1_4zxvA.pdb.gz
8	4x28D1	0.48	3.93	0.092	0.785	model1_4x28D1.pdb.gz
9	1jqiA	0.48	3.90	0.022	0.785	model1_1jqiA.pdb.gz
10	4ktoA1	0.48	4.00	0.032	0.804	model1_4ktoA1.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:0044822	1.00	poly(A) RNA binding
GO:0042162	1.00	telomeric DNA binding
GO:0004004	1.00	ATP-dependent RNA helicase activity
GO:0003682	1.00	chromatin 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:0044699	1.00	single-organism process
GO:0000184	1.00	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0044249	0.61	cellular biosynthetic process
GO:0009059	0.61	macromolecule biosynthetic process
GO:0034645	0.60	cellular macromolecule biosynthetic process
GO:0050794	0.55	regulation of cellular process
GO:0048856	0.55	anatomical structure development
GO:0044767	0.55	single-organism developmental process
GO:0043009	0.54	chordate embryonic development
GO:0044763	0.52	single-organism cellular process
GO:0080090	0.51	regulation of primary metabolic process
GO:0060255	0.51	regulation of macromolecule metabolic process
GO:0031323	0.51	regulation of cellular metabolic process
GO:2000112	0.50	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.50	regulation of nitrogen compound metabolic process
GO:0044710	0.50	single-organism metabolic process
GO:0010468	0.50	regulation of gene expression

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:0005654	1.00	nucleoplasm
GO:0032991	0.66	macromolecular complex
GO:0043226	0.64	organelle
GO:0043229	0.63	intracellular organelle
GO:0030529	0.62	intracellular ribonucleoprotein complex
GO:0043227	0.60	membrane-bounded organelle
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0005634	0.58	nucleus
GO:0044444	0.55	cytoplasmic part
GO:0043234	0.53	protein complex
GO:0005681	0.53	spliceosomal complex
GO:0044427	0.51	chromosomal part
GO:0044530	0.50	supraspliceosomal complex
GO:0035145	0.50	exon-exon junction complex
GO:0000785	0.50	chromatin
GO:0000784	0.50	nuclear chromosome, telomeric region

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	0.474	3.94	0.043	0.785	1.3.99.7	NA
2	0.060	1rx0A	0.471	4.21	0.061	0.813	1.3.99.-	NA
3	0.060	1siqA	0.458	3.98	0.020	0.776	1.3.99.7	42,75
4	0.060	1ivhA	0.488	3.96	0.065	0.804	1.3.99.10	NA
5	0.060	1bucB	0.456	4.26	0.067	0.794	1.3.99.2	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	1pwqA	0.472	4.17	0.082	0.776	0.17	SD2	complex1.pdb.gz	30,41,43,83
2	0.01	2vigD	0.481	3.91	0.023	0.785	0.12	FAD	complex2.pdb.gz	33,34,78,83
3	0.01	2vigA	0.484	3.99	0.023	0.794	0.12	FAD	complex3.pdb.gz	82,84,89,93
4	0.01	1pwqB	0.471	4.27	0.091	0.794	0.20	SD2	complex4.pdb.gz	49,60,62,89,92
5	0.01	1yqyA	0.385	4.60	0.047	0.701	0.22	915	complex5.pdb.gz	31,50,76,84,99
6	0.01	1pwvA	0.473	4.15	0.082	0.785	0.11	III	complex6.pdb.gz	78,79,82,92,100
7	0.01	1pwuA	0.472	4.23	0.071	0.785	0.15	GM6	complex7.pdb.gz	32,57,81,82,91

	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.