D-I-TASSER Q9HAZ2-D3

D-I-TASSER results for Q9HAZ2-D3

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

Input Sequence in FASTA format

>Q9HAZ2 (83 residues)
PLTPSPMMDKAKPSPSLNHASLGFNEYFPSRPHPGSLPFSTAPPTFPALTPGFPGIFPPS
LYPRPPLLPPTSLLKSPLNHTQD

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| PLTPSPMMDKAKPSPSLNHASLGFNEYFPSRPHPGSLPFSTAPPTFPALTPGFPGIFPPSLYPRPPLLPPTSLLKSPLNHTQD
Prediction	CCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	98888531236789877778875132178889999886888999888789888877887678899989997544586654579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| PLTPSPMMDKAKPSPSLNHASLGFNEYFPSRPHPGSLPFSTAPPTFPALTPGFPGIFPPSLYPRPPLLPPTSLLKSPLNHTQD
Prediction	83574443554444442444332235314444444414144444424433442322234423453432354631543354468
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
PLTPSPMMDKAKPSPSLNHASLGFNEYFPSRPHPGSLPFSTAPPTFPALTPGFPGIFPPSLYPRPPLLPPTSLLKSPLNHTQD

2ldmA

0.04

1.86

0.62

CEthreader

FQINEQVLASWSDSRFYPAKVTAVNDGTYTVKFYDGVVQTVKHIHVKAFSKDQNIVGNARGSRAHSSHLSKKG----------

3zf7P2

0.07

2.92

0.67

EigenThreader

STDFERYQLRVAKRSRAYWARKIFDENDKKNPV--SWHKVALKKLLKNAKKVDSTPAAKKRVEKARAARKARLAAGKSKTKV-

7abiK

0.11

3.88

0.38

FFAS-3D

-LTEEERRAELRANGKVITNKAVKGKYFLQKYYHRGAFFMDEDEEV--YKRDFSAPTLEDHFNK-TILPKVMQVKNFGRSGRT

3boiA

0.07

0.06

2.53

1.62

SPARKS-K

DGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP--------

4h04A

0.15

0.04

1.22

0.71

CNFpred

---------------------------------------------------------------RPATVPSMDGWTDGTGAWTL

1kv9A

0.04

1.93

0.83

DEthreader

DPEVAKVKARTSCPYAFNFADATQAKLYGFCVCH-LI-P-DLRQSTREFQQIVLGPSFD-SLKEVEQKLYVMSREYEDYMARH

7as9E

0.10

3.57

0.95

MapAlign

IELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGEVRMITVRGSVMNPNDHPHGGGEGRAPIGRKSPMSPWGKPTLGF---

2mk0A

0.21

0.20

6.51

0.92

MUSTER

PSQPSDCGEVIEECPIDACFLPKSDSARPPDCTAVGRPDCNVLP-FPN-NIGCPSCCPFECSPDNPMFTPSPDGSPPNSPTML

2pffB

0.24

0.23

7.12

0.49

HHsearch

PNTSLPENNEGVPSPMLSISNLTQEDYAPSGLDQSRIPFSERKLK-----FSNRFLPVASPFHSHLLVPASDLIKNNVSFNAK

3hxjA

0.05

2.30

0.56

CEthreader

LYAINTDGTEKWRFKTKKAIYATPIVSTIYVGSNDNYLYAIRFKTNDAITSAASIGKDGTIYFGSDKVYAINPDGTEKWNFYA

(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	0.5267

(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	4u83A	0.48	3.91	0.024	0.843	model1_4u83A.pdb.gz
2	3owaA	0.47	4.14	0.073	0.843	model1_3owaA.pdb.gz
3	1sirA	0.46	4.03	0.012	0.843	model1_1sirA.pdb.gz
4	3wiqA1	0.46	3.95	0.042	0.831	model1_3wiqA1.pdb.gz
5	1h54B1	0.44	3.83	0.043	0.807	model1_1h54B1.pdb.gz
6	1g6q11	0.40	3.57	0.042	0.639	model1_1g6q11.pdb.gz
7	1ivhA1	0.39	4.44	0.069	0.831	model1_1ivhA1.pdb.gz
8	2c0uA	0.39	4.01	0.095	0.747	model1_2c0uA.pdb.gz
9	1r2jA1	0.39	4.30	0.030	0.735	model1_1r2jA1.pdb.gz
10	1is2A	0.38	4.64	0.070	0.771	model1_1is2A.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:0003677	1.00	DNA binding
GO:0043565	0.74	sequence-specific DNA binding
GO:0008134	0.74	transcription factor binding
GO:0003712	0.74	transcription cofactor activity
GO:0033613	0.73	activating transcription factor binding
GO:0003713	0.73	transcription coactivator activity
GO:0003824	0.60	catalytic activity
GO:0016740	0.55	transferase activity
GO:0008168	0.53	methyltransferase activity
GO:0018024	0.52	histone-lysine N-methyltransferase activity

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:0065007	0.93	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0050794	0.92	regulation of cellular process
GO:0006355	0.90	regulation of transcription, DNA-templated
GO:0045892	0.89	negative regulation of transcription, DNA-templated
GO:0048518	0.80	positive regulation of biological process
GO:0048522	0.79	positive regulation of cellular process
GO:0009893	0.79	positive regulation of metabolic process
GO:0006357	0.79	regulation of transcription from RNA polymerase II promoter
GO:0048583	0.78	regulation of response to stimulus
GO:0045893	0.78	positive regulation of transcription, DNA-templated
GO:0023051	0.78	regulation of signaling
GO:0010646	0.78	regulation of cell communication
GO:0009968	0.77	negative regulation of signal transduction
GO:0009987	0.74	cellular process
GO:0000122	0.69	negative regulation of transcription from RNA polymerase II promoter
GO:0045595	0.67	regulation of cell differentiation
GO:0030512	0.67	negative regulation of transforming growth factor beta receptor signaling pathway
GO:0044767	0.64	single-organism developmental process
GO:0044763	0.64	single-organism cellular process
GO:0048856	0.63	anatomical structure development
GO:0032501	0.62	multicellular organismal process
GO:0044707	0.61	single-multicellular organism process
GO:0048869	0.58	cellular developmental process
GO:2000026	0.57	regulation of multicellular organismal development
GO:0051241	0.57	negative regulation of multicellular organismal process
GO:0030154	0.57	cell differentiation
GO:0002682	0.57	regulation of immune system process
GO:0050873	0.56	brown fat cell differentiation
GO:0043457	0.56	regulation of cellular respiration
GO:0030853	0.56	negative regulation of granulocyte differentiation

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:0043231	1.00	intracellular membrane-bounded organelle
GO:0044444	0.82	cytoplasmic part
GO:0005634	0.76	nucleus
GO:0043234	0.75	protein complex
GO:0044422	0.61	organelle part
GO:0044446	0.60	intracellular organelle part
GO:0044428	0.53	nuclear part
GO:0017053	0.52	transcriptional repressor complex
GO:0005654	0.50	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	3d0oB	0.306	4.89	0.048	0.675	1.1.1.27	NA
2	0.060	1rp1A	0.383	4.13	0.058	0.735	3.1.1.3	NA
3	0.060	2vjyA	0.429	3.80	0.070	0.795	4.1.1.1	NA
4	0.060	1f0iA	0.326	4.48	0.052	0.675	3.1.4.4	NA
5	0.060	1rwlA	0.404	3.87	0.033	0.723	2.7.11.1	22

	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	3ijeA	0.439	3.78	0.116	0.783	0.41	UUU	complex1.pdb.gz	23,52,54
2	0.01	3euj0	0.422	3.58	0.093	0.735	0.43	III	complex2.pdb.gz	54,55,56
3	0.01	3qdvA	0.449	3.99	0.042	0.819	0.40	A2G	complex3.pdb.gz	9,26,27
4	0.01	3owaB	0.447	4.26	0.048	0.855	0.40	FAD	complex4.pdb.gz	20,22,24,53,56

	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.