D-I-TASSER Q9NX61-D1

D-I-TASSER results for Q9NX61-D1

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

Input Sequence in FASTA format

>Q9NX61 (231 residues)
MAVLGVQLVVTLLTATLMHRLAPHCSFARWLLCNGSLFRYKHPSEEELRALAGKPRPRGR
KERWANGLSEEKPLSVPRDAPFQLETCPLTTVDALVLRFFLEYQWFVDFAVYSGGVYLFT
EAYYYMLGPAKETNIAVFWCLLTVTFSIKMFLTVTRLYFSAEEGGTRPHLQAYLCLAKAR
VEQLRREAGRIEAREIQQRVVRVYCYVTVVSLQYLTPLILTLNCTLLLKTL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MAVLGVQLVVTLLTATLMHRLAPHCSFARWLLCNGSLFRYKHPSEEELRALAGKPRPRGRKERWANGLSEEKPLSVPRDAPFQLETCPLTTVDALVLRFFLEYQWFVDFAVYSGGVYLFTEAYYYMLGPAKETNIAVFWCLLTVTFSIKMFLTVTRLYFSAEEGGTRPHLQAYLCLAKARVEQLRREAGRIEAREIQQRVVRVYCYVTVVSLQYLTPLILTLNCTLLLKTL
Prediction	CCCSSHHHHHHHHHHHHHHHHHHHHCHHHHSSSCCCSSSSCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCSSSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHHHHHHHCCCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHSSCCCCCSSHHHHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	971003699999999999997554132230454372689718997999997099887542100003788787513136564120102366655101122344667776563421000136677863476211112468999999999999999999981315888524168899999999999999716523376764456545788899999999999999999986319
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MAVLGVQLVVTLLTATLMHRLAPHCSFARWLLCNGSLFRYKHPSEEELRALAGKPRPRGRKERWANGLSEEKPLSVPRDAPFQLETCPLTTVDALVLRFFLEYQWFVDFAVYSGGVYLFTEAYYYMLGPAKETNIAVFWCLLTVTFSIKMFLTVTRLYFSAEEGGTRPHLQAYLCLAKARVEQLRREAGRIEAREIQQRVVRVYCYVTVVSLQYLTPLILTLNCTLLLKTL
Prediction	522132010310211020220033231120000222031021023640372165447665553446555665302013616040552404432122042144030102022100001000211220233442110000101103311330021002110315543433202110110352055036324414434144301100100000002221003011200012326
	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                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCSSHHHHHHHHHHHHHHHHHHHHCHHHHSSSCCCSSSSCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCSSSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHHHHHHHCCCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHSSCCCCCSSHHHHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
MAVLGVQLVVTLLTATLMHRLAPHCSFARWLLCNGSLFRYKHPSEEELRALAGKPRPRGRKERWANGLSEEKPLSVPRDAPFQLETCPLTTVDALVLRFFLEYQWFVDFAVYSGGVYLFTEAYYYMLGPAKETNIAVFWCLLTVTFSIKMFLTVTRLYFSAEEGGTRPHLQAYLCLAKARVEQLRREAGRIEAREIQQRVVRVYCYVTVVSLQYLTPLILTLNCTLLLKTL

7ad3B

0.08

3.08

0.46

CEthreader

RCGAAALTLIVMWMTSRSRKTPIFIINQVSLFLIILHKYLLSNYSSVTYALTGFPQFISRGDVHVYGATNIIQVLLVASIETSLQIKVIFTGDNFKRIGLMLTSISFTLGIATVTMYFVSAVKGMIVTQDKYFNASTILLASSINFMSFVLVVKLILAIRSRFHILLIMSCQSLLVPSIIFILAYSLKPNQGTDVLTTVATLLAVLSLPLSSMWATAANNASKTN------

6rkoA

0.07

0.06

2.33

0.77

EigenThreader

RLGKVQHMCVTWLVALGSNLSALWILVANGWMQNPIASDFNFETM--------------------------------------RMEMVSFSELVLVAQVKFVHTVASGYVTGAMFILGISAWYMLKGRDFAFAKRSFAIAASFGMAAVLSVIVLKLAAIEM------VQHEERIRNGMKAYSLLEQLRSVRDQFNSMKKDLGYGLLLKAFRIMVACGFLLLAIIALSFWSV

5z1fA1

0.11

0.10

3.46

0.83

FFAS-3D

FGSFLVSLGTSFVIFVILMLL---FTWLS-----------RKSGNAPIYYPNRILKGLEPWEGTSLTRN---------PFAWMREALTSSEQDVVNLSGVDTAVHFVFLSTVLGIFACSSLLLLPTLLPLGAVYWISLVTYFFLWKAYKHVSSLRAQALMSADMIINLLATSLPKSATFFLTYVALKFFIGYGLELSRTRVPGDMLILTITFCYIAPLILITYFGLGW---

6tbuA4

0.06

2.46

0.71

SPARKS-K

-----------KKSINRFCQMFEECITKSIMNYAYLWLLIFGALGASSAVIVFWYPGLQLPEKSHFQLFSDLKFTLSHDTFVAICLAMAASLAVLLCFTVNILISIYAVLTVSLSIFNTVAVLILLGWQLNI--LESIAVSTAIGLAVDFSLHYGIHYRMSPVKERAATQFVLSRIIGPTVMAATTTGSNILPYIQIGVFLVVVMIVSWFYATFFLMSLLRVAGPQHGFLE

2yevA

0.12

0.10

3.65

0.85

CNFpred

LFFFIIQAGLTGFGNFVVPLMLGARDVALPRVNAFSYWAFL-GAIVLALMSYFFPGGAPS---------------------GWTFYYPFSAQSESGVDFYLAAILLLGFSSLLGNANFVATIYNLRAMSLWKMPIYVWSVFAASVLNLFSLAGLT---------------AATLLVLLERKIGLSWFNPVGGDPVLFQQFFWFYSHPTVYVMLLPYLGILAEVASTFARKP

6c70A

0.07

0.06

2.30

0.83

DEthreader

------SHPLFAESNARFHALAITKM--L---C----AT-FSSWTGITFI--EDSPR----AMSGAGHVALI--------------------NSLDVLFCSWLLFACEQLQHLKAIMKPLMELSATGLQEMLVRSAIKYWVERHKHVVRLVTAVGDAYGVALLLHMLT----T-TITLTLLAYQATKV--Y-AT-IGYLLYTLGQVFLFCIFGNRLIEESSSVMEAAYSWV

3rkoM1

0.07

0.06

2.55

0.76

MapAlign

--LPWLILIPFIGGFLCWQTERFGVKPRWIALITMGLTLSLLWLQGGYQWQSEFDMPWIPRFGI-------SIHLAI--DGLSLVVLTGLLGVLAVLCSWKEIEKYQGFFHLNLMWILGGVIGVFLALFFFFWEMMLVPMYFLIALAATKFFIYTQASG--------LVMLIAILALVFVHYNATGVW-TFNYEELLNTEYLLMLGFFIAFAVKGWLPDAHSQASVDLAGI

5cwmA

0.13

0.12

4.18

0.47

MUSTER

------------DPEDELKRVEKLVKEAEELLRQAK------GSEEDLEKALRTAEEREAKKVLEQAEKEGDPEVALRAVELVVRVAELLLRIAKESGSEEALERALRVAEEAARLAKRVLELAEKQGDPEVALRAVELVVRVAELLLRIAKESSEEALER----ALRVAEEAARLAKRVLELAEKQGDPEVARRAVELVKRVAELLERIARESGSEEAKERAERVREEAR

1vt4I3

0.08

0.04

1.74

0.52

HHsearch

-----------------------EYALHRSIVDH------------------------------------------------YNIPKTFDSDDLIPPYLDQYFYSHIGPERMTLFVFLDFRLEQKIRHDSTAWNA-----SGSILNTLQQL----KFYKPYICDNDPKYERL----VNAILDFLPKIE-----------ENLICSKYTDLLRIAL----MAEDEAIFEEAH

7jroc

0.09

0.08

3.12

0.43

CEthreader

LIFILYTMFVWWRDVLRESTLEGHHTKVVQLGLRYGFILFIVSEVMFLFAFFWAFFHSSLAPTVEIGGIWPPLGIW-------------------VLDPWEIPFLNTLILLSSGAAVTWAHHAILAGKEKRAVYALVATVLLALVFTGFQGMEYYQAPFTISDSIYGHGFHVIIGTLFLIICGIRQYLGHLTKEHHVGFEAAAWYWHFVDVVWLFLFVSIYWWGGI-----

(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	0.6114

(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	6r3qA1	0.53	5.03	0.061	0.792	model1_6r3qA1.pdb.gz
2	6c70A	0.51	5.36	0.065	0.801	model1_6c70A.pdb.gz
3	4mt1A	0.48	5.16	0.082	0.732	model1_4mt1A.pdb.gz
4	6r4lA	0.48	5.24	0.037	0.736	model1_6r4lA.pdb.gz
5	6ajfA3	0.47	5.11	0.053	0.727	model1_6ajfA3.pdb.gz
6	4acrA	0.47	5.83	0.062	0.805	model1_4acrA.pdb.gz
7	6tbuA	0.47	5.38	0.072	0.745	model1_6tbuA.pdb.gz
8	6wjlG	0.47	5.88	0.052	0.801	model1_6wjlG.pdb.gz
9	6lr0U	0.47	5.64	0.052	0.788	model1_6lr0U.pdb.gz
10	7cq5C	0.47	5.87	0.060	0.783	model1_7cq5C.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:1901681	0.37	sulfur compound binding
GO:0050840	0.37	extracellular matrix binding
GO:0046914	0.37	transition metal ion binding
GO:0043394	0.37	proteoglycan binding
GO:0019838	0.37	growth factor 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:1902230	1.00	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
GO:0045739	1.00	positive regulation of DNA repair
GO:0034644	1.00	cellular response to UV
GO:0034599	1.00	cellular response to oxidative stress
GO:0032526	1.00	response to retinoic acid

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:0016021	1.00	integral component of membrane
GO:0016020	1.00	membrane
GO:0044464	0.74	cell part
GO:0005886	0.68	plasma membrane

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	1mhsA	0.429	5.51	0.053	0.706	3.6.3.6	NA
2	0.060	1ug9A	0.332	6.43	0.031	0.615	3.2.1.70	45,182
3	0.060	1ffuB	0.423	5.41	0.054	0.688	1.2.99.2	NA
4	0.060	3ixzA	0.456	5.32	0.063	0.732	3.6.3.10	NA
5	0.060	1qhaA	0.418	5.16	0.033	0.636	2.7.1.1	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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.