D-I-TASSER Q92831-D1

D-I-TASSER results for Q92831-D1

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

Input Sequence in FASTA format

>Q92831 (206 residues)
MSEAGGAGPGGCGAGAGAGAGPGALPPQPAALPPAPPQGSPCAAAAGGSGACGPATAVAA
AGTAEGPGGGGSARIAVKKAQLRSAPRAKKLEKLGVYSACKAEESCKCNGWKNPNPSPTP
PRADLQQIIVSLTESCRSCSHALAAHVSHLENVSEEEMNRLLGIVLDVEYLFTCVHKEED
ADTKQVYFYLFKLLRKSILQRGKPVV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSEAGGAGPGGCGAGAGAGAGPGALPPQPAALPPAPPQGSPCAAAAGGSGACGPATAVAAAGTAEGPGGGGSARIAVKKAQLRSAPRAKKLEKLGVYSACKAEESCKCNGWKNPNPSPTPPRADLQQIIVSLTESCRSCSHALAAHVSHLENVSEEEMNRLLGIVLDVEYLFTCVHKEEDADTKQVYFYLFKLLRKSILQRGKPVV
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence	98667788877776777788877789865456788877886767678888899888888888888998532577899998774298212356521323235788751257889999988654311022221023211278847899986566898999999999999999998862468811678899999999999997258889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSEAGGAGPGGCGAGAGAGAGPGALPPQPAALPPAPPQGSPCAAAAGGSGACGPATAVAAAGTAEGPGGGGSARIAVKKAQLRSAPRAKKLEKLGVYSACKAEESCKCNGWKNPNPSPTPPRADLQQIIVSLTESCRSCSHALAAHVSHLENVSEEEMNRLLGIVLDVEYLFTCVHKEEDADTKQVYFYLFKLLRKSILQRGKPVV
Prediction	75644442423233233444344434444464544466244344545654544444464444445455463344245245424614444405621432415346514042134464445464552442134035305404231441054057364730340021012043023214465345122001100410240025354347
	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                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
MSEAGGAGPGGCGAGAGAGAGPGALPPQPAALPPAPPQGSPCAAAAGGSGACGPATAVAAAGTAEGPGGGGSARIAVKKAQLRSAPRAKKLEKLGVYSACKAEESCKCNGWKNPNPSPTPPRADLQQIIVSLTESCRSCSHALAAHVSHLENVSEEEMNRLLGIVLDVEYLFTCVHKEEDADTKQVYFYLFKLLRKSILQRGKPVV

6r4lA

0.06

0.05

2.10

0.83

DEthreader

QGKLKTLLFFVVTLLLKVPEGLRISFNSKENNNDISTVSYMFLYAWALRTRFTHYDRNIIAIGRMPSILMSLLCQTGCFLIAAFVTM-----------------------FSAWF-----F--TSLVFLPEIQF------MALLGIS--LN---A-VSLVNLIICVGLGVEFCVHISLTIESVIKGITLTKFIGVVLIFDVFYF-W

7by1A1

0.74

0.43

12.25

2.94

SPARKS-K

---------------------------------------------------------------------------SQRKAQVRGLPRAKKLEKLGVFSACKANETCKCNGWKNPKPPPAANL----------SELCRSCEHPLADHVSHLENVSEDEINRLLGMVVDVENLFMSVHKEEDTDTKQVYFYLFKLLRKCILQMTRPVV

6bx3F

0.10

0.09

3.38

0.59

MUSTER

VNDIWSRLKTDEDRAQTGHIDKGQLDFIDNNIVVKTDDEKEIFDQIVVRDMTLKTLEDDLQEVQEISLPLFKKKLELLEVYLGWLDNVYTEMRKLDDDAASHVECGKC-GYSTYERIPCSVEEGSNEEATKIHEVCWKCNHLVSTNQEQY----LQQIDSLESMQERLQHLIQARKK---QLNIQYYEEILR--------------

7by1A1

0.73

0.43

12.12

1.26

MapAlign

----------------------------------------------------------------------------QRKAQVRGLPRAKKLEKLGVFSACKANETCKCNGWKNP----------KPPPAANLSELCRSCEHPLADHVSHLENVSEDEINRLLGMVVDVENLFMSVHKEEDTDTKQVYFYLFKLLRKCILQMTRPVV

7by1A1

0.71

0.42

11.86

1.13

CEthreader

---------------------------------------------------------------------------SQRKAQVRGLPRAKKLEKLGVFSACKANETCKCNGWK----------NPKPPPAANLSELCRSCEHPLADHVSHLENVSEDEINRLLGMVVDVENLFMSVHKEEDTDTKQVYFYLFKLLRKCILQMTRPVV

7by1A

0.74

0.44

12.38

5.80

HHsearch

---------------------------------------------------------------------------SQRKAQVRGLPRAKKLEKLGVFSACKANETCKCNGWKNPKPPP----------AANLSELCRSCEHPLADHVSHLENVSEDEINRLLGMVVDVENLFMSVHKEEDTDTKQVYFYLFKLLRKCILQMTRPVV

7by1A1

0.74

0.44

12.38

1.70

FFAS-3D

---------------------------------------------------------------------------SQRKAQVRGLPRAKKLEKLGVFSACKANETCKCNGWKNPKPPPAA----------NLSELCRSCEHPLADHVSHLENVSEDEINRLLGMVVDVENLFMSVHKEEDTDTKQVYFYLFKLLRKCILQMTRPVV

7by1A1

0.72

0.42

11.99

0.75

EigenThreader

---------------------------------------------------------------------------SQRKAQVRGLPRAKKLEKLGVFSACKANETCKCNGWK------NPKPP----PAANLSELCRSCEHPLADHVSHLENVSEDEINRLLGMVVDVENLFMSVHKEEDTDTKQVYFYLFKLLRKCILQMTRPVV

6xteA

0.08

0.04

1.52

0.51

CNFpred

--------------------------------------------------------------------------AKELKEGFVE-YTEQVVKLMVPLLKFYFHDGVRVAA-----------------------------AESMPLLLECARVRGPEYLTQMWHFMC--DALIKAIGTE---PDSDVLSEIMHSFAKCIEVMGDGCL

6tntA

0.04

0.03

1.69

0.83

DEthreader

PDAYHCQPASDWPEACL--GQ-SKCEGNLPSQDSNGHLTIEMTSIG--DVPHQEYCTDRSIKEINVDVTCPATFLRTLARCLIWILFRFAGSLSLAMVMAG----SGNLKVLQCRF-------------------L-FLGGG--RYS-LS------TSNSSIAALLCALY-PH-FPA-HSTDNRYHLQALRH-LYVLAAEPR----

(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	0.5937

(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	7by1A	0.58	0.93	0.736	0.587	model1_7by1A.pdb.gz
2	6kswC	0.45	5.47	0.040	0.752	model1_6kswC.pdb.gz
3	6ifkA	0.45	5.86	0.054	0.806	model1_6ifkA.pdb.gz
4	6mcpA2	0.44	5.19	0.056	0.728	model1_6mcpA2.pdb.gz
5	3cskA	0.44	5.33	0.055	0.704	model1_3cskA.pdb.gz
6	3kcfC	0.44	5.20	0.081	0.694	model1_3kcfC.pdb.gz
7	1lwwA	0.44	5.59	0.047	0.757	model1_1lwwA.pdb.gz
8	3fvyA2	0.38	5.51	0.036	0.636	model1_3fvyA2.pdb.gz
9	1cm8A	0.37	5.66	0.061	0.626	model1_1cm8A.pdb.gz
10	1irkA	0.35	5.19	0.033	0.587	model1_1irkA.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	0.89	catalytic activity
GO:0004402	0.88	histone acetyltransferase activity
GO:0003682	0.88	chromatin binding
GO:0019899	0.85	enzyme binding
GO:0042826	0.73	histone deacetylase binding
GO:0008134	0.73	transcription factor binding
GO:0003713	0.73	transcription coactivator activity
GO:1901363	0.51	heterocyclic compound binding
GO:0097159	0.51	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:0008152	0.95	metabolic process
GO:0044260	0.94	cellular macromolecule metabolic process
GO:0044238	0.94	primary metabolic process
GO:0016043	0.92	cellular component organization
GO:0006464	0.92	cellular protein modification process
GO:0018393	0.91	internal peptidyl-lysine acetylation
GO:0050794	0.90	regulation of cellular process
GO:0080090	0.81	regulation of primary metabolic process
GO:0060255	0.81	regulation of macromolecule metabolic process
GO:0031323	0.81	regulation of cellular metabolic process
GO:0006325	0.81	chromatin organization
GO:0048522	0.80	positive regulation of cellular process
GO:0043966	0.80	histone H3 acetylation
GO:0009893	0.80	positive regulation of metabolic process
GO:0010604	0.79	positive regulation of macromolecule metabolic process
GO:2000112	0.70	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.70	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.70	regulation of gene expression
GO:0031325	0.69	positive regulation of cellular metabolic process
GO:0006807	0.69	nitrogen compound metabolic process
GO:0006355	0.69	regulation of transcription, DNA-templated
GO:0090304	0.68	nucleic acid metabolic process
GO:0010628	0.68	positive regulation of gene expression
GO:0006338	0.68	chromatin remodeling
GO:1901576	0.67	organic substance biosynthetic process
GO:0044249	0.67	cellular biosynthetic process
GO:0016070	0.67	RNA metabolic process
GO:0006357	0.67	regulation of transcription from RNA polymerase II promoter
GO:0032774	0.66	RNA biosynthetic process
GO:0045893	0.58	positive regulation of transcription, DNA-templated
GO:0050896	0.57	response to stimulus
GO:0051716	0.56	cellular response to stimulus
GO:0045944	0.56	positive regulation of transcription from RNA polymerase II promoter
GO:0031399	0.56	regulation of protein modification process
GO:0010033	0.56	response to organic substance
GO:0071495	0.55	cellular response to endogenous stimulus
GO:0071310	0.55	cellular response to organic substance
GO:0006109	0.55	regulation of carbohydrate metabolic 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:0044446	0.94	intracellular organelle part
GO:0044428	0.93	nuclear part
GO:0043231	0.93	intracellular membrane-bounded organelle
GO:0032991	0.93	macromolecular complex
GO:0005634	0.86	nucleus
GO:0043234	0.84	protein complex
GO:1990234	0.81	transferase complex
GO:0044451	0.81	nucleoplasm part
GO:0005671	0.80	Ada2/Gcn5/Ada3 transcription activator complex
GO:0070461	0.60	SAGA-type complex
GO:0005654	0.58	nucleoplasm

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	1iasA	0.444	5.22	0.087	0.694	2.7.11.30 2.7.1.37	112,115,133
2	0.060	3npkA	0.417	4.94	0.087	0.612	2.5.1.10	165
3	0.060	2h8oA	0.426	5.06	0.072	0.641	2.5.1.10	NA
4	0.060	1dizA	0.417	5.30	0.060	0.694	3.2.2.21	NA
5	0.060	3jvpD	0.417	5.70	0.031	0.714	2.7.1.16	148

	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	2wotA	0.435	5.10	0.051	0.680	0.17	ZZG	complex1.pdb.gz	68,69,72,73,74,77,80,165
2	0.01	1yqmA	0.439	5.31	0.053	0.723	0.14	UUU	complex2.pdb.gz	164,168,189,191,192,193
3	0.01	1b6c1	0.374	5.63	0.039	0.660	0.20	III	complex3.pdb.gz	158,159,162,163,166,167
4	0.01	1yqrA	0.442	5.57	0.047	0.757	0.16	UUU	complex4.pdb.gz	79,94,149
5	0.01	3faaB	0.438	5.48	0.067	0.704	0.18	55F	complex5.pdb.gz	150,197,200
6	0.01	1yqlA	0.441	5.45	0.053	0.743	0.13	UUU	complex6.pdb.gz	98,99,164,195,196
7	0.01	1n39A	0.441	5.48	0.054	0.748	0.27	UUU	complex7.pdb.gz	97,98,110,111,145,149

	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.