D-I-TASSER Q9H267-D3

D-I-TASSER results for Q9H267-D3

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

Input Sequence in FASTA format

>Q9H267 (113 residues)
SQVVYEGLVDDTFRIKCGSVDFGPEVTSSDKSLKVLLNAEDKVFNEIRNEHFSNVFGFLS
QKARNLQAQYDRRRGMDIKQMKNFVSQELKGLKQEHRLLSLHIGACESIMKKK

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| SQVVYEGLVDDTFRIKCGSVDFGPEVTSSDKSLKVLLNAEDKVFNEIRNEHFSNVFGFLSQKARNLQAQYDRRRGMDIKQMKNFVSQELKGLKQEHRLLSLHIGACESIMKKK
Prediction	CCCHHHHHHHHHHCCCCCSSSSCCCCCCCCCCSSSSCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	96028899999846479979856888888754587579989899998751399999999999999999996212278999999999998999999986999999999998649
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| SQVVYEGLVDDTFRIKCGSVDFGPEVTSSDKSLKVLLNAEDKVFNEIRNEHFSNVFGFLSQKARNLQAQYDRRRGMDIKQMKNFVSQELKGLKQEHRLLSLHIGACESIMKKK
Prediction	74331200020114154340404764557655242404771610451244214401630352055136536756553254025104631551474464243012004303758
	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

CCCHHHHHHHHHHCCCCCSSSSCCCCCCCCCCSSSSCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
SQVVYEGLVDDTFRIKCGSVDFGPEVTSSDKSLKVLLNAEDKVFNEIRNEHFSNVFGFLSQKARNLQAQYDRRRGMDIKQMKNFVSQELKGLKQEHRLLSLHIGACESIMKKK

4jc8A

0.28

0.27

8.12

1.33

DEthreader

TQLTYEGLIDEYFGIQNNQTDVDAVIVGA-RKRKIQLDGSDSLYSQLRDANFAIVGSLLNTVARRLKSDYES--R--TAELKEFVK-KLPGYQAEQQSLKIHSNIAEEIINYT

4bx8A2

0.27

0.25

7.61

1.87

SPARKS-K

--LTYEGLIDEIYGIQNSYVKLPPEKALPTEAKKLQLNSAEELYAEIRDKNFNAVGSVLSKKAKIISAAFEERHNKQF-------VSQLPHMQAARGSLANHTSIAELIKDVT

4bx8A

0.27

0.26

7.87

1.16

MapAlign

TQLTYEGLIDEIYGIQNSYVKLPPEKFLPTEAKKLQLNSAEELYAEIRDKNFNAVGSVLSKKAKIISAAFEER-------HNKQFVSQLPHMQAARGSLANHTSIAELIKDVT

4bx8A

0.27

0.26

7.87

1.07

CEthreader

TQLTYEGLIDEIYGIQNSYVKLPPEKFLPTEAKKLQLNSAEELYAEIRDKNFNAVGSVLSKKAKIISAAFEERHNKQ-------FVSQLPHMQAARGSLANHTSIAELIKDVT

4bx8A2

0.29

0.27

8.09

1.92

MUSTER

--LTYEGLIDEIYGIQNSYVKLPPEKFAPTEAKKLQLNSAEELYAEIRDKNFNAVGSVLSKKAKIISAAFEERHNK------QFV-SQLPHMQAARGSLANHTSIAELIKDVT

2xheA

0.16

5.29

2.64

HHsearch

HELTYQAAAYDLLNIENDIYSYSTVDAGREQQRQVVLGEDDDIWLQMRHLHISEVFRKVKSSFDEFCVSARRLQEGGAGALKQMLK-DLPQHREQMQKYSLHLDMSNAINMAF

4bx8A2

0.27

0.25

7.59

1.70

FFAS-3D

--LTYEGLIDEIYGIQNSYVKLPPEKALPTEAKKLQLNSAEELYAEIRDKNFNAVGSVLSKKAKIISAAFEERHNKQF-------VSQLPHMQAARGSLANHTSIAELIKD--

4bx8A2

0.27

0.25

7.61

1.30

EigenThreader

--LTYEGLIDEIYGIQNSYVKLPPEKFAPTEAKKLQLNSAEELYAEIRDKNFNAVGSVLSKKAKIISAAFEERHNK-------QFVSQLPHMQAARGSLANHTSIAELIKDVT

2xheA

0.17

5.53

1.06

CNFpred

HELTYQAAAYDLLNIENDIYSYSTVDGGREQQRQVVLGEDDDIWLQMRHLHISEVFRKVKSSFDEFCVSARRLQGGGAGALKQMLK-DLPQHREQMQKYSLHLDMSNAINMAF

4bx8A

0.30

0.27

8.34

1.33

DEthreader

TQLTYEGLIDEIYGIQNSYVKLPPEKFA-TEAKKLQLNSAEELYAEIRDKNFNAVGSVLSKKAKIISAAFEERHN----K--QFV-SQLPHMQAARGSLANHTSIAELIKDVT

(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	0.8273

(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	4bx8A	0.87	1.20	0.292	0.929	model1_4bx8A.pdb.gz
2	4jc8A	0.86	1.46	0.280	0.947	model1_4jc8A.pdb.gz
3	6xjlA	0.73	2.01	0.146	0.850	model1_6xjlA.pdb.gz
4	1mqsA2	0.72	1.87	0.122	0.832	model1_1mqsA2.pdb.gz
5	2xheA	0.70	2.37	0.165	0.867	model1_2xheA.pdb.gz
6	3c98A3	0.70	1.97	0.165	0.814	model1_3c98A3.pdb.gz
7	4ccaA2	0.70	2.36	0.173	0.832	model1_4ccaA2.pdb.gz
8	2pjxA2	0.58	1.68	0.176	0.655	model1_2pjxA2.pdb.gz
9	1epuA	0.57	2.90	0.207	0.752	model1_1epuA.pdb.gz
10	1u7mA	0.40	1.71	0.075	0.469	model1_1u7mA.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:1901363	0.43	heterocyclic compound binding
GO:0097159	0.43	organic cyclic compound binding
GO:0032555	0.38	purine ribonucleotide binding
GO:0032550	0.38	purine ribonucleoside binding
GO:0035639	0.36	purine ribonucleoside triphosphate binding
GO:0000149	0.35	SNARE binding
GO:0019905	0.30	syntaxin 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:0006810	0.90	transport
GO:0009987	0.82	cellular process
GO:0044699	0.75	single-organism process
GO:0006996	0.74	organelle organization
GO:0051641	0.69	cellular localization
GO:0016192	0.69	vesicle-mediated transport
GO:0071702	0.67	organic substance transport
GO:0015031	0.66	protein transport
GO:0044763	0.62	single-organism cellular process
GO:0007033	0.58	vacuole organization
GO:0061025	0.53	membrane fusion
GO:0051648	0.53	vesicle localization
GO:0032418	0.52	lysosome localization
GO:0032400	0.52	melanosome localization
GO:0016050	0.52	vesicle organization

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:0044464	0.98	cell part
GO:0044424	0.97	intracellular part
GO:0044444	0.95	cytoplasmic part
GO:0043227	0.85	membrane-bounded organelle
GO:0043234	0.82	protein complex
GO:0043231	0.80	intracellular membrane-bounded organelle
GO:0044425	0.78	membrane part
GO:0098796	0.76	membrane protein complex
GO:0016020	0.75	membrane
GO:0044446	0.74	intracellular organelle part
GO:0005773	0.72	vacuole
GO:0044437	0.67	vacuolar part
GO:0031090	0.67	organelle membrane
GO:0098588	0.66	bounding membrane of organelle
GO:0098805	0.64	whole membrane
GO:0005774	0.63	vacuolar membrane
GO:0005768	0.63	endosome
GO:0048471	0.61	perinuclear region of cytoplasm
GO:0005770	0.61	late endosome
GO:0000323	0.61	lytic vacuole
GO:0031982	0.59	vesicle
GO:0031410	0.58	cytoplasmic vesicle
GO:0030897	0.58	HOPS complex
GO:0005764	0.57	lysosome
GO:0031988	0.54	membrane-bounded vesicle
GO:0044440	0.53	endosomal part
GO:0016023	0.53	cytoplasmic, membrane-bounded vesicle
GO:0005737	0.53	cytoplasm
GO:0031091	0.52	platelet alpha granule

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	1rsrB	0.583	3.87	0.028	0.867	1.17.4.1	NA
2	0.060	1rqgA	0.534	3.38	0.073	0.735	6.1.1.10	NA
3	0.060	2vuxB	0.396	2.96	0.052	0.549	1.17.4.1	NA
4	0.060	1chuA	0.507	3.90	0.040	0.752	1.4.3.16	NA
5	0.060	2rccA	0.578	3.90	0.087	0.894	1.17.4.1	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	0.06	3pujA	0.730	1.90	0.163	0.867	0.37	III	complex1.pdb.gz	6,10,37,38
2	0.01	1biqA	0.585	3.79	0.019	0.858	0.34	UUU	complex2.pdb.gz	6,9,102,109
3	0.01	3ablP	0.559	3.28	0.067	0.743	0.17	CDL	complex3.pdb.gz	8,109,110
4	0.01	3b96A	0.575	3.22	0.072	0.735	0.12	MYA	complex4.pdb.gz	6,10,37,39
5	0.01	3ablC	0.559	3.57	0.058	0.761	0.12	UUU	complex5.pdb.gz	4,8,12
6	0.01	2eijC	0.560	3.68	0.058	0.770	0.13	CDL	complex6.pdb.gz	3,9,10,47
7	0.01	2dyrP	0.560	3.68	0.058	0.770	0.12	CDL	complex7.pdb.gz	3,8,9,18
8	0.01	1v55C	0.560	3.68	0.058	0.770	0.16	CDL	complex8.pdb.gz	8,20,105
9	0.01	3ee40	0.560	3.26	0.063	0.796	0.10	III	complex9.pdb.gz	53,56,57,60,61,63,64,67,71,73,74

	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.