D-I-TASSER Q9C0D6-D5

D-I-TASSER results for Q9C0D6-D5

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

Input Sequence in FASTA format

>Q9C0D6 (242 residues)
LENTEAELHLLFVRTKSLKENIQRDGELCQQMEDFLQFAIEKLRELECWKQELQDEAYTL
IDFFCEDKKTMKLDECFQIFRDFCTKFNKSLGSAQSPPLSPLALGIKEHELVTGLAQFNL
QGSQGMEETSQLTLSDFSPMELESVGHRGPQSLSASSSSLTPMGRDALGSLSPALEDGKA
APDEPGSAALGSVGSSDPENKDPRPLFCISDTTDCSLTLDCSEGTDSRPRGGDPEEGGEG
DG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| LENTEAELHLLFVRTKSLKENIQRDGELCQQMEDFLQFAIEKLRELECWKQELQDEAYTLIDFFCEDKKTMKLDECFQIFRDFCTKFNKSLGSAQSPPLSPLALGIKEHELVTGLAQFNLQGSQGMEETSQLTLSDFSPMELESVGHRGPQSLSASSSSLTPMGRDALGSLSPALEDGKAAPDEPGSAALGSVGSSDPENKDPRPLFCISDTTDCSLTLDCSEGTDSRPRGGDPEEGGEGDG
Prediction	CHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	27899999999999999999722352599999999999999999999999999999999999985797869899999999999999999999998079999999999999999999764115653011011330114754222322122121123533345444555445664333466677788776667777888777888985343677776423357788777888888543588889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| LENTEAELHLLFVRTKSLKENIQRDGELCQQMEDFLQFAIEKLRELECWKQELQDEAYTLIDFFCEDKKTMKLDECFQIFRDFCTKFNKSLGSAQSPPLSPLALGIKEHELVTGLAQFNLQGSQGMEETSQLTLSDFSPMELESVGHRGPQSLSASSSSLTPMGRDALGSLSPALEDGKAAPDEPGSAALGSVGSSDPENKDPRPLFCISDTTDCSLTLDCSEGTDSRPRGGDPEEGGEGDG
Prediction	67414530550453055136505746503620350054036205504521640461054006101424740414300410440152045026515646445444544554345535536465664565455343643454545424454355164455345745455564545446655444644655544546554474564334222432233324043764554645754456556688
	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                 120                 140                 160                 180                 200                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
LENTEAELHLLFVRTKSLKENIQRDGELCQQMEDFLQFAIEKLRELECWKQELQDEAYTLIDFFCEDKKTMKLDECFQIFRDFCTKFNKSLGSAQSPPLSPLALGIKEHELVTGLAQFNLQGSQGMEETSQLTLSDFSPMELESVGHRGPQSLSASSSSLTPMGRDALGSLSPALEDGKAAPDEPGSAALGSVGSSDPENKDPRPLFCISDTTDCSLTLDCSEGTDSRPRGGDPEEGGEGDG

3na7A

0.10

0.07

2.62

0.59

CEthreader

VSKNEQTLQDTNAKIASIQKKMSEIERELRSLNIEEDIAKERSNQANREIENLQNEIKRKSEKQEDLKK--EMLELEKLALELESLVENEV----------------------KNIKETQQIIFKKKEDLVEK----------------------------------TEPKIYSFYERIRRWAKNTSIVTIKKQACGGCFIRLNDKIYTEVLTSGDMITCPYCGRILYAEGA----------

1u4qA

0.05

2.29

0.50

EigenThreader

GKDLLKKHQLLEADISAHLNSQADSLMKRETINGRFQRIKSMAAARRAKLNESHRLHQFFRDMDDEESWIKEKKLLVSAHEPAIQGVLDTGKKLSDDNTIGKEEIQQRLAQFVDHWKELKQLAAARGQRLEESLEYQQFVANVEEEEAWINEKMTLVASEDYGDTLAAIQGLLKKHEAFETDFTVHKDRVNDVCANGEDLIKKNNHH-----------VENITAKMKGLKGKVSDLEKAAAQ

1v9dB2

0.20

0.07

2.39

0.83

FFAS-3D

AENLQKSLDQMKKQIADVERDVQNKDKFVEKMTSFVKDAQEQYNKLRMMHSNMETLYKELGDYFVFDPKKLSVEEFFMDLHNFRNMFLQAVK------------------------------------------------------------------------------------------------------------------------------------------------------

1v9dB

0.17

0.08

2.57

0.83

SPARKS-K

AENLQKSLDQMKKQIADVERDVQNFPKFVEKMTSFVKDAQEQYNKLRMMHSNMETLYKELGDYFVFDPKKLSVEEFFMDLHNFRNMFLQAVKENQKRRETEEKMRRAKL-------------------------------------------------------------------------------------------------------------------------------------

2z6eA

0.18

0.07

2.16

0.76

CNFpred

MTELDKEISTLRSGLKAVETELEY-DKFVSVVSQFITVASFSFSDVEDLLAEAKDLFTKAVKHFGEEAGKIQPDEFFGIFDQFLQAVSEAKQ------------------------------------------------------------------------------------------------------------------------------------------------------

7bspA

0.08

0.06

2.40

0.67

DEthreader

INAFLIVYLFILLTKAAVCTTLKYVWQSTND----FLSFMVLFNFII--PVSMYVTVEMQKFLGSF--NTSDL--NEE-----------------------LGQVDYVFTDKTGTLTENS-----------QDQAAETIEALHAAGLKVWVLLELTTKT-IEESERKEDRLLLRLICKCTAVLCKLSIG------------------GIKAANSDYSVHLKL--IDTSDPRLYMISMDTRFW

2rgrA

0.05

2.45

0.84

MapAlign

MIMTDQDHDGSHIKGLIINFLESSDKDYIDLAFDFINKELILFSLADNIRSGQRKVLYGCFKYVSECTAYHGEQSLAQTIIGLAQLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGATYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGRIEQIGDNVLEITLISPISLMNMVAFDPHGKIKKYN

5nnvA

0.11

0.10

3.59

0.60

MUSTER

ELAESSAISAKEAKIEDTRDKIQALDESVDELQQVLLVTSEELEKLEGRKEVLKERKKNAVQNQEQ------LEEAIVQFQQKETVLKEELSKQEAVFETLQAEVKQLRAQVKEKQQLSNELTELKIAAAKKEQACKGEEDNLARLKKELTETELALKEAKEDLSFLTSESSSTSGEEKLEEAAKHKLNDKTKTIELIALRRD------------QHGLDTYERELKEKRLYKQKTTLL---

1v9dB2

0.19

0.08

2.53

1.68

HHsearch

AENLQKSLDQMKKQIADVERDVQNKDKFVEKMTSFVKDAQEQYNKLRMMHSNMETLYKELGDYFVFDPKKLSVEEFFMDLHNFRNMFLQAVKEMRRAKL-----------------------------------------------------------------------------------------------------------------------------------------------

4iloA

0.09

0.06

2.38

0.49

CEthreader

IKGGEKRIQEISDQINKLENQQAAVMDEFNALTQEMTAANKERRTLEHQLSDLMDKQAGSEDLLISLKESLSSTENSSSAIEEEIRENIRKINEEGRSLLSQRTQLKETTDPELFSVYERLLNNKKDRVVVPIENRVCSGCHIALTPQHENLVRKQDHLVFCEHCSRILYWQ----------------------------------------------------------------------

(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

SpinHigh qualityWhite background

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4648

(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

script 1 started

FileManager.getAtomSetCollectionFromFile(model1_4av3A.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q9C0D6/Q9C0D6-D5/model1_4av3A.pdb.gz

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The Resolver thinks Pdb

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Time for openFile(model1_4av3A.pdb.gz): 3494 ms

reading 8535 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

8535 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

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SpinHigh qualityWhite background

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	4av3A	0.46	5.70	0.049	0.752	model1_4av3A.pdb.gz
2	4a01A	0.46	5.60	0.051	0.719	model1_4a01A.pdb.gz
3	6r9tA	0.45	6.02	0.050	0.781	model1_6r9tA.pdb.gz
4	1n5uA	0.45	5.30	0.052	0.686	model1_1n5uA.pdb.gz
5	2pffA3	0.44	6.55	0.090	0.831	model1_2pffA3.pdb.gz
6	3hmjA6	0.44	6.38	0.038	0.810	model1_3hmjA6.pdb.gz
7	2uv9D	0.44	6.57	0.083	0.831	model1_2uv9D.pdb.gz
8	6rohA	0.44	6.34	0.043	0.797	model1_6rohA.pdb.gz
9	6xljD	0.44	6.13	0.039	0.756	model1_6xljD.pdb.gz
10	1ocrN	0.44	5.17	0.041	0.682	model1_1ocrN.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:0008092	0.60	cytoskeletal protein binding
GO:0003779	0.55	actin 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	0.91	single-organism process
GO:0009987	0.63	cellular process
GO:0044767	0.57	single-organism developmental process
GO:0044763	0.57	single-organism cellular process
GO:0050794	0.55	regulation of cellular 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:0044464	0.99	cell part
GO:0044424	0.91	intracellular part
GO:0044444	0.70	cytoplasmic part
GO:0005737	0.60	cytoplasm
GO:0043226	0.55	organelle
GO:0044446	0.53	intracellular organelle part
GO:0043229	0.52	intracellular organelle

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

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FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q9C0D6/Q9C0D6-D5/model1.pdb.gz

The Resolver thinks Pdb

Time for openFile(model1.pdb.gz): 1023 ms

reading 3609 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

3609 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

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SpinHigh qualityWhite background

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	1e6yE	0.415	5.69	0.048	0.678	2.8.4.1	NA
2	0.060	1dquA	0.398	5.94	0.060	0.661	4.1.3.1	NA
3	0.060	1xmeA	0.408	5.43	0.018	0.657	1.9.3.1	NA
4	0.060	1pj6A	0.399	6.36	0.031	0.715	1.5.3.10	NA
5	0.060	2vycA	0.402	6.09	0.070	0.711	4.1.1.19	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

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script 1 started

FileManager.getAtomSetCollectionFromFile(complex1.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q9C0D6/Q9C0D6-D5/complex1.pdb.gz

The Resolver thinks Pdb

Time for openFile(complex1.pdb.gz): 1181 ms

reading 3634 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

3634 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

8535 atoms selected

4926 atoms selected

3609 atoms selected

ambientPercent = 40

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SpinHigh qualityWhite background

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	2bxmA	0.449	5.33	0.052	0.686	0.45	IMN	complex1.pdb.gz	83,86,87,92,101,102,105,106
2	0.01	2ydfA	0.414	4.87	0.042	0.612	0.40	IO3	complex2.pdb.gz	102,103,106,107
3	0.01	3a73B	0.448	5.21	0.052	0.678	0.41	PJ2	complex3.pdb.gz	87,91,103,106
4	0.01	2vdbA	0.443	5.06	0.049	0.669	0.43	NPS	complex4.pdb.gz	81,84,106,109
5	0.01	2xvwA	0.449	5.26	0.052	0.682	0.41	9NR	complex5.pdb.gz	84,87,93,103,106,107
6	0.01	1e7cA	0.450	5.34	0.052	0.686	0.62	HLT	complex6.pdb.gz	91,100,105
7	0.01	3cx9A	0.448	5.38	0.052	0.686	0.47	MYR	complex7.pdb.gz	87,91,99,104
8	0.01	1e7bA	0.413	5.03	0.042	0.616	0.41	HLT	complex8.pdb.gz	84,87,88,92,100,104

	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.