D-I-TASSER Q8N1V2-D3

D-I-TASSER results for Q8N1V2-D3

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

Input Sequence in FASTA format

>Q8N1V2 (132 residues)
NVIFSRCRDEMFMTAGNGTIRVWELDLPNRKIWPTECQTGQLKRIVMSIGVDDDDSFFYL
GTTTGDILKMNPRTKLLTDVGPAKDKFSLGVSAIRCLKMGGLLVGSGAGLLVFCKSPGYK
PIKKIQLQGGIT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| NVIFSRCRDEMFMTAGNGTIRVWELDLPNRKIWPTECQTGQLKRIVMSIGVDDDDSFFYLGTTTGDILKMNPRTKLLTDVGPAKDKFSLGVSAIRCLKMGGLLVGSGAGLLVFCKSPGYKPIKKIQLQGGIT
Prediction	CSSSSCCCCCSSSSSCCCSSSSSSSSCCCCSSSSSSSCCCCSSSSSSSSSSCCCCCSSSSSCCCCCSSSSSCCCCCSSCCCCCCCCCCCCSSSSSSSCCCCSSSSSCCCSSSSSSCCCCSSSSSSSSCCCCC
Confidence	936626999889993699699999928778162487303544788999999599988999628755899985887201014554320673689999189988997279769999768870768988625569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| NVIFSRCRDEMFMTAGNGTIRVWELDLPNRKIWPTECQTGQLKRIVMSIGVDDDDSFFYLGTTTGDILKMNPRTKLLTDVGPAKDKFSLGVSAIRCLKMGGLLVGSGAGLLVFCKSPGYKPIKKIQLQGGIT
Prediction	804334444220000144402003034754504445153352433030030266241000103312001020534125511443532432020020156430000123230210437625324515155438
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSCCCCCSSSSSCCCSSSSSSSSCCCCSSSSSSSCCCCSSSSSSSSSSCCCCCSSSSSCCCCCSSSSSCCCCCSSCCCCCCCCCCCCSSSSSSSCCCCSSSSSCCCSSSSSSCCCCSSSSSSSSCCCCC
NVIFSRCRDEMFMTAGNGTIRVWELDLPNRKIWPTECQTGQLKRIVMSIGVDDDDSFFYLGTTTGDILKMNPRTKLLTDVGPAKDKFSLGVSAIRCLKMGGLLVGSGAGLLVFCKSPGYKPIKKIQLQGGIT

4j87A

0.10

3.62

1.50

DEthreader

CAAFHPSE-DLIVSASDQTVRVWDISGLKADAIVKFVLE-GHDRGVNWCAFHPTLPLILSAGDDRLVKLWRMTKAWEVDT-CR--GHFNNVSCCLFHPQELILSASEDKTIRVWDLNRRTAVQTFRRNDRFW

2ce8A2

0.13

0.12

4.22

1.69

SPARKS-K

SCKLLP-DGCTLIVGGASTLSIWDLAAPTPR---IKAELTSSAPACYALAISPDSKVCFSCCSDGNIAVWDLHNQTLVRQFQG---HTDGASCIDISNDGKLWTGGLDNTVRSWDLREGRQLQQHDFTSQIF

5o9zL

0.15

0.14

4.82

0.32

MapAlign

CMCFSRD-TEMLATGAQGKIKVWKIQ---SGQCLRRFER-AHSKGVTCLSFSKDSSQILSASFDQTIRIHGLKSGKTLKEFR---GHSSFVNEATFTQDGYIISASSDGTVKIWNMKTTECSNTFKI-TVNS

5mzhA

0.08

2.98

0.26

CEthreader

AIAFNNPYGDKIVTGSDKTCKLWDAYTG-----QLYYTLKGHQTEIVCLSFNPQSTIIATGSMDNTAKLWDVETGQERATLA---GHRAEIVSLGFNTGGLIVTGSFDHDSRLWDVRTGQCVHVLGHRGEVS

2ce8A2

0.12

0.11

4.02

1.65

MUSTER

SCKLLPDGCTLIVGGEASTLSIWDLAAPTP---RIKAELTSSAPACYALAISPDSKVCFSCCSDGNIAVWDLHNQTLVRQF---QGHTDGASCIDISNDGTLWTGGLDNTVRSWDLREGRQLQQHDFTSQIF

3dm0A

0.14

0.13

4.42

0.60

HHsearch

DVVLSSD-GQFALSGSDGELRLWDLAAGVSTRR-----FVGHTKDVLSVAFSLDNRQIVSASRDRTIKLWNTL-GECKYTIEGGEGHRDWVSCVRFSPNTTIVSASWDKTVKVWNLSNCKLRSTLAHTGYVS

4lg8A2

0.12

0.11

3.98

1.46

FFAS-3D

GLSLHATGDYLLSSSDDQYWAFSDIQTGRVLTKVT---DETSGCSLTCAQFHPDGLIFGTGTMDSQIKIWDLKERTNVANFP---GHSGPITSIAFSENGYLATAADDSSVKLWDLRKLKNFKTLQ------

6zwmC2

0.10

3.64

0.52

EigenThreader

SAHID-PDASYMAAVNTGNCYVWNLTEVTQLIPKTKIPA--HTRYALQCRFSPDSTLLATCSADQTCKIWRSNFSLMTELSIKSGNSRGWMWGCAFSGDSQYVTASSDNLARLWCVETGEIKREYGHQKAVV

4nsxA

0.11

0.10

3.59

1.86

CNFpred

GISLDGMNRKMVSCGLDGIVGFYDFNKSTLLGKLKL------DAPITAMVYHRSSDLFALALDDLSIVVIDAVTQRVVRQLW---GHSNRITAFDFSPERWIVSASLDSTIRTWDLPTGGCIDGIIVDNVAT

3j80g

0.11

3.83

1.50

DEthreader

SLSTSAAQPNLLVSGSDKTLISWRLTENEQQGVPVRSYK-GHSHIVQDVVVSADGNYAVSASWDKTLRLWNLATGNSE-ARF-V-GHTGDVLSVAIDANSKIISASRDKTIRVWNT-VGDCAYVLLHTDWVT

(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	0.8476

(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	4j87A	0.89	1.27	0.111	0.955	model1_4j87A.pdb.gz
2	3j80g	0.89	1.32	0.103	0.955	model1_3j80g.pdb.gz
3	3fm0A	0.89	1.43	0.087	0.955	model1_3fm0A.pdb.gz
4	5vh9B	0.89	1.28	0.127	0.955	model1_5vh9B.pdb.gz
5	4d6vA	0.89	1.11	0.129	0.939	model1_4d6vA.pdb.gz
6	1vyhT	0.88	1.04	0.089	0.932	model1_1vyhT.pdb.gz
7	5nrlH	0.88	1.41	0.079	0.962	model1_5nrlH.pdb.gz
8	3jcrD	0.88	1.15	0.137	0.939	model1_3jcrD.pdb.gz
9	4lg8A	0.88	1.23	0.112	0.947	model1_4lg8A.pdb.gz
10	6zmtj	0.88	1.16	0.161	0.939	model1_6zmtj.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	0.68	heterocyclic compound binding
GO:0097159	0.68	organic cyclic compound binding
GO:0003676	0.59	nucleic acid binding
GO:0003677	0.52	DNA 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	0.90	cellular process
GO:0008152	0.79	metabolic process
GO:0044237	0.78	cellular metabolic process
GO:0044260	0.77	cellular macromolecule metabolic process
GO:0044238	0.77	primary metabolic process
GO:0006139	0.71	nucleobase-containing compound metabolic process
GO:0016070	0.70	RNA metabolic process
GO:0065007	0.61	biological regulation
GO:0044249	0.61	cellular biosynthetic process
GO:0009059	0.61	macromolecule biosynthetic process
GO:0071840	0.60	cellular component organization or biogenesis
GO:0044271	0.60	cellular nitrogen compound biosynthetic process
GO:0050789	0.59	regulation of biological process
GO:0034645	0.59	cellular macromolecule biosynthetic process
GO:0050794	0.58	regulation of cellular process
GO:0044699	0.57	single-organism process
GO:0016043	0.57	cellular component organization
GO:0044763	0.50	single-organism cellular process
GO:0019222	0.50	regulation of metabolic 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:0044424	1.00	intracellular part
GO:0043226	0.96	organelle
GO:0043229	0.95	intracellular organelle
GO:0043227	0.94	membrane-bounded organelle
GO:0044446	0.93	intracellular organelle part
GO:0043231	0.92	intracellular membrane-bounded organelle
GO:0032991	0.91	macromolecular complex
GO:0005634	0.88	nucleus
GO:0044428	0.80	nuclear part
GO:0043234	0.80	protein complex
GO:0044444	0.65	cytoplasmic part

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	0.066	1rwlA	0.775	2.15	0.099	0.917	2.7.11.1	NA
2	0.060	1fwxA	0.829	1.61	0.049	0.932	1.7.99.6	NA
3	0.060	1qksB	0.792	2.30	0.120	0.947	1.7.2.1	NA
4	0.060	1lrwA	0.798	2.32	0.120	0.947	1.1.99.8	NA
5	0.060	1eusA	0.723	3.10	0.076	1.000	3.2.1.18	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	0.09	3pslB	0.857	1.14	0.142	0.909	0.61	III	complex1.pdb.gz	45,46,47,90,91,92,107,131
2	0.03	1a0rB	0.860	1.51	0.096	0.947	0.74	FAR	complex2.pdb.gz	90,91,104,106,108,109,111,113
3	0.03	2xl2A	0.871	1.39	0.113	0.939	0.50	III	complex3.pdb.gz	55,57,58,80,96,98,118
4	0.03	1omw3	0.887	1.19	0.096	0.947	0.50	III	complex4.pdb.gz	42,45,47,63,64,66,82,87,89,90,92,107,130
5	0.03	2bcj5	0.883	1.22	0.096	0.947	0.51	III	complex5.pdb.gz	17,18,42,44,45,47,63,90,92

	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.