D-I-TASSER Q9NZB2-D2

D-I-TASSER results for Q9NZB2-D2

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

Input Sequence in FASTA format

>Q9NZB2 (208 residues)
IKIAVSIEDEANKDLPPAALLYRPVRQYVYGVLFSLAESRKKTERLAFRKNRLPPEFSPV
IIKEWAAYKGKSPQTPELVEALAFREWTCPNLKRLWLGKAVEDKNRRMRAFLACMRSDTP
AMLNPANVPTHLMVLCCVLRYMVQWPGARILRRQELDAFLAQALSPKLYEPDQLQELKIE
NLDPRGIQLSALFMSGVDMALFANDACG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| IKIAVSIEDEANKDLPPAALLYRPVRQYVYGVLFSLAESRKKTERLAFRKNRLPPEFSPVIIKEWAAYKGKSPQTPELVEALAFREWTCPNLKRLWLGKAVEDKNRRMRAFLACMRSDTPAMLNPANVPTHLMVLCCVLRYMVQWPGARILRRQELDAFLAQALSPKLYEPDQLQELKIENLDPRGIQLSALFMSGVDMALFANDACG
Prediction	CCCCCCSCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCSSSSSSSSCCCCCCCCCSSCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
Confidence	9776410134676678546766599999999985413445566654311357888899936888877489999997351252579999997211116898379999999999997899978850124885799999999999972485312499978999999722679989985235688785134599999953378887403679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| IKIAVSIEDEANKDLPPAALLYRPVRQYVYGVLFSLAESRKKTERLAFRKNRLPPEFSPVIIKEWAAYKGKSPQTPELVEALAFREWTCPNLKRLWLGKAVEDKNRRMRAFLACMRSDTPAMLNPANVPTHLMVLCCVLRYMVQWPGARILRRQELDAFLAQALSPKLYEPDQLQELKIENLDPRGIQLSALFMSGVDMALFANDACG
Prediction	6614010124245612221200220123000001224534543554535556455643200010011247442531520522406726214043012465273443304000200436135204334133201000000100142361530343303000010013413427304605266045300200211130021002013218
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCSCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCSSSSSSSSCCCCCCCCCSSCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
IKIAVSIEDEANKDLPPAALLYRPVRQYVYGVLFSLAESRKKTERLAFRKNRLPPEFSPVIIKEWAAYKGKSPQTPELVEALAFREWTCPNLKRLWLGKAVEDKNRRMRAFLACMRSDTPAMLNPANVPTHLMVLCCVLRYMVQWPGARILRRQELDAFLAQALSPKLYEPDQLQELKIENLDPRGIQLSALFMSGVDMALFANDACG

7cq5C

0.07

2.94

0.51

CEthreader

RINHTAFRTVEIKRWVICALIGILTGLVACFIDIVVENLAGLKYRVIKGNIDKFTEKGGLSFSLLLWATLNAAFVLVGSVIVVAAGSGIPQIKCFLNGVKIPHVVRLKTLVIKVSGVIL-SVVGGLAVGKEGPMIHSGSVIAAGISQGRSTSLKRDFKIFEYFRRDTEKRLFSLEEGASFWNQFLTWRIFFASMISTFTLNFVLSIYH

6zu9o

0.09

0.08

3.16

0.63

EigenThreader

ATPSTGVELKKGKLLKDGLHQYKKLIARKFIDLVESKIASEQTRADELQKQEIDASYRAVLDLL-----RNNALLEITYSGVVKKTMHFCLKYMLRQHLDAANYQDQRFQQVDVSVLWHEAYRSIEDVSTLANYYENLVKVF----FVSGDPLLHTTAWKKFYKLYSTNPRYRLLNLDAKPTRKEMLQSIIEDVIMRRVFVAASQKFT

5xjcV2

0.08

0.05

2.06

0.58

FFAS-3D

----------------------VSFRRTIYLAIQSSLDFEECAHK----------------------------------------------LLKM--EFPESQTKELCNMILDCCAQQRTYEKFFGLLAGRFSFEGIFKEQYDTIHRLETNKLRNVAKMFAHLLYTDSWSVLECIKLSEETTTSSSRIFVKIFFQELCEYM-------

4m5dA2

0.09

0.08

3.11

0.65

SPARKS-K

FFQDVILEFETSPKWPDEITSLEKAKTAFLLKIQEELSANSSTYRSFFSRDESIPYNLEIVTLNILT------PEGYGFKFRVLTERDEILYLRAIANELKPELEATFLKFTAKYLA-SVRHTRTHSYQFYSPVVRLFKRWLDTHLLLGHITDELAELIAIKPFVDPA---------PYFIPGS----LENGFLKVLKFISQWNWKDD

4b8jA

0.15

0.10

3.38

0.68

CNFpred

-----------------------EVLTDACWALSYLSDG-----------------------------------TNDKIQAVI--AGVCPRLVELLLHPSPSVLIPALRTVGNIVTGDDAQTQCII-----HQALPCLLSLLTQN--KKSIKKEACWTISNITAG----NKDQIQAVINAGIIGPLVNLLQTKKEAAWAISNATSGGS

3sqgA

0.04

0.03

1.45

0.83

DEthreader

--------------------M--AWDDM-KRG-IV--LG--LDDAHGLEARVGEFAAKVQSNYMP--------VKRARSHNE-------------G----------I--AD--ST-R---SPALFPNDP-IRAELESIAVAAMVQLGFTASATYTDNILEDFCYKGCEIGIIAENDYLTYEAGGSVRACCGHSAYAGLVAGA-WVLSP

6sciA

0.08

0.07

2.86

0.74

MapAlign

--PFAVVTDDATGQKYPLLCAFGGLDAVTHAMEAYVSVLASEFSDGQALQ--------ALLLYLASYHEGSKNPVARVAAAGAFANAFLCHSMAHKLGFHIPHGLANALLICNVIIADHLGLS-APGDRTAAKIEKLLAWLETLKAELGIVQEADFLANVDKLSEDAFDDQCTGANPRY----PLISELKQILLDTYYGRDYVE----

5fvcA2

0.14

0.13

4.44

0.45

MUSTER

KESQYTIKRDVGTAVTP-SSLQQEITLLCGEILYAKHADYKYAAEIGIQSTALGSERVQQILRN----SGSE------VQVVLTRTYDIHGVEKSWVEEIDKEARKTMATLLKESSGNIPQNQRPSA-PDTPIILLCVGALIFTKLASTI--EVGLETTVRRANRVLSDALKRYPRMDIPKIARSFYDLFEQKVYHRSLFIEYGKALG

2pffB

0.16

0.15

4.97

0.66

HHsearch

KILPEPTEGFAAEPTTPAELVGKFLGYVSSLVEPSKVG-QFDQVNLIKNMAKRP-FDKKSNSALFRAVGEGNAQL-VAIFGGQGNTDYFEELRDLYQTYHVLGDLIKFSTLSELINILEW-LENPSNTPDSIPISCPLAHYVVTAK-LLGFTPGELRSYLKGAHSQGLVTAVAIAETD-SWESFFVSVRKVLFFIG------VRCYEA

7cq5C1

0.06

2.68

0.48

CEthreader

RINHTAFRTVEIKRWVICALIGILTGLVACFIDIVVENLAGLKYRVIKGNIDIVAFIEPVAAGSGIPQIKCFLNGVKIPHVVRLKTLVIKVSGVILSVVGGLAVGKEGPMIHSGSVIAAGISQGRSTSLKRDFKIFEYFRRDTEK--RDFVSAGAAAGVSAAFGAPVGGVLFSLEEGASFWNQFLTWRIFFASMISTFTLNFVLSIYH

(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	0.7001

(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	6lodF	0.47	5.03	0.051	0.745	model1_6lodF.pdb.gz
2	6f0kF	0.47	5.13	0.034	0.745	model1_6f0kF.pdb.gz
3	6btmC	0.46	4.43	0.040	0.663	model1_6btmC.pdb.gz
4	3ebgA	0.45	5.02	0.036	0.745	model1_3ebgA.pdb.gz
5	6oiuA	0.45	5.57	0.062	0.784	model1_6oiuA.pdb.gz
6	4z24A	0.45	5.61	0.040	0.755	model1_4z24A.pdb.gz
7	6lodC	0.45	5.19	0.043	0.740	model1_6lodC.pdb.gz
8	6l47A	0.45	4.81	0.027	0.668	model1_6l47A.pdb.gz
9	4tlvA	0.45	5.33	0.084	0.750	model1_4tlvA.pdb.gz
10	5b43A	0.44	5.31	0.034	0.712	model1_5b43A.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	0.84	heterocyclic compound binding
GO:0097159	0.84	organic cyclic compound binding
GO:0003676	0.82	nucleic acid binding
GO:0003723	0.80	RNA binding
GO:0044822	0.78	poly(A) RNA 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	1.00	cellular process
GO:0007165	1.00	signal transduction
GO:0008152	0.84	metabolic process
GO:0044237	0.83	cellular metabolic process
GO:0044238	0.82	primary metabolic process
GO:0043170	0.82	macromolecule metabolic process
GO:0044260	0.81	cellular macromolecule metabolic process
GO:0019538	0.76	protein metabolic process
GO:0048518	0.74	positive regulation of biological process
GO:0006464	0.74	cellular protein modification process
GO:0065009	0.73	regulation of molecular function
GO:0051049	0.73	regulation of transport
GO:0035556	0.73	intracellular signal transduction
GO:0006468	0.73	protein phosphorylation
GO:2000021	0.72	regulation of ion homeostasis
GO:0051928	0.72	positive regulation of calcium ion transport
GO:0032414	0.72	positive regulation of ion transmembrane transporter 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 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:0016020	0.70	membrane
GO:0005737	0.66	cytoplasm

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	1n1zA	0.426	5.41	0.085	0.697	5.5.1.8	159
2	0.060	1lvlA	0.432	5.63	0.067	0.755	1.8.1.4	NA
3	0.060	2qaeA	0.428	5.48	0.076	0.712	1.8.1.4	NA
4	0.060	3kvnX	0.423	5.10	0.060	0.668	3.1.1.1	NA
5	0.060	1frvB	0.419	5.64	0.054	0.712	1.12.2.1	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	0.01	3b2pA	0.332	6.28	0.036	0.649	0.15	ARG	complex1.pdb.gz	158,159,189,190,193
2	0.01	1zkqA	0.426	5.63	0.035	0.731	0.10	FAD	complex2.pdb.gz	1,19,32,109,110
3	0.01	3q43A	0.373	5.96	0.075	0.663	0.19	D66	complex3.pdb.gz	140,193,196,197,200,201,204
4	0.01	2yajC	0.360	4.46	0.029	0.524	0.11	4HP	complex4.pdb.gz	2,141,142
5	0.01	3ebiA	0.373	5.87	0.075	0.659	0.15	BEY	complex5.pdb.gz	192,196,199,200
6	0.01	2zxgA	0.434	5.72	0.039	0.740	0.12	S23	complex6.pdb.gz	136,139,140,155
7	0.01	1n1zA	0.426	5.41	0.085	0.697	0.19	POP	complex7.pdb.gz	23,188,192,196
8	0.01	1v59A	0.430	5.47	0.076	0.721	0.18	NAD	complex8.pdb.gz	159,196,197,198
9	0.01	2rabA	0.425	5.54	0.047	0.731	0.12	NAD	complex9.pdb.gz	27,28,29,32

	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.