D-I-TASSER A6NDP7-D2

D-I-TASSER results for A6NDP7-D2

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

Input Sequence in FASTA format

>A6NDP7 (152 residues)
VSSYMATVSGLLKIVQAFVACIIFGALVHDSRYGRYVATQWCVAVYSLCFLATVAVVALS
VMGHTGGLGCPFDRLVVVYTFLAVLLYLSAAVIWPVFCFDPKYGEPKRPPNCARGSCPWD
SQLVVAIFTYVNLLLYVVDLAYSQRIRFVPSL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VSSYMATVSGLLKIVQAFVACIIFGALVHDSRYGRYVATQWCVAVYSLCFLATVAVVALSVMGHTGGLGCPFDRLVVVYTFLAVLLYLSAAVIWPVFCFDPKYGEPKRPPNCARGSCPWDSQLVVAIFTYVNLLLYVVDLAYSQRIRFVPSL
Prediction	CCCCCCCHHHHHHHHHHHHHHHHHHHSCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCSSCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHSSSSSCC
Confidence	96301001379999999999993331106301268650121368999999999999999851447643466234799999999999999998731012143349999999998877841123357889999999999999987122554269
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VSSYMATVSGLLKIVQAFVACIIFGALVHDSRYGRYVATQWCVAVYSLCFLATVAVVALSVMGHTGGLGCPFDRLVVVYTFLAVLLYLSAAVIWPVFCFDPKYGEPKRPPNCARGSCPWDSQLVVAIFTYVNLLLYVVDLAYSQRIRFVPSL
Prediction	74033333331332323310020000002443155420120002011303331221000111524420213143013131330131133023001001037636746336714433031132000001033123313112331222333358
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCHHHHHHHHHHHHHHHHHHHSCCCCCCCCCCCSSSHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCSSCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHSSSSSCC
VSSYMATVSGLLKIVQAFVACIIFGALVHDSRYGRYVATQWCVAVYSLCFLATVAVVALSVMGHTGGLGCPFDRLVVVYTFLAVLLYLSAAVIWPVFCFDPKYGEPKRPPNCARGSCPWDSQLVVAIFTYVNLLLYVVDLAYSQRIRFVPSL

3rkoB

0.09

0.07

2.54

1.03

CNFpred

------TPVSALIHAATMVTAGVYLIARTHGL--FLMTPEVLHLVGIVGAVTLLLAGFAALVQT-------DIKRVLAYSTMSQIGYMFLALGVQA---------------------WDAAIFHLMTHAFFKALLFLASGSVILACHHEQNI

5vjsA

0.05

2.19

1.33

DEthreader

--QQ-AQEFQQLLQEIQQLGRELLKGELQGKLRQILEDEEKHIELLETLQQTGQEAQQLLQELQQTLQKQQLAQKIQQLLQKHQQLGAKILEDEEKHIELLE--TILGGDELR---ELLKGELQGIKQYRELQQLGQKAQQLVQKLQQTGQK

6akfA

0.12

0.10

3.49

0.79

CEthreader

------SMSMGLEITGTSLAVLGWLCTIVCCLQAARALIVVSILLAAFGLLVALVGAQATNAVQD-------ETAKAKITIVAGVLFLLAALLTLVAVSWSANTIIRDFYNPLVPEAGLYVGWAAAALQLLGGALLAAS-------------

6m02A

0.11

3.82

0.88

EigenThreader

GLRLELAVDKMVTCIAVGLPLLLISLAFCWAAVLPLWLHKFFPYILLLFAILLYLPPLFWRFAAAPHILIIKYISCRLLTLIIILLACIYLGYYFSLSSLSDKSGILRNDSTVPDQAVGIFQLLSVINLVVYVLLAPVVVYTL----FVPFR

6yofA2

0.11

0.09

3.31

0.68

FFAS-3D

-------FQSLNPLFIMLYTPFFAWLWTAWKKNQPSSPTKFAVGLMFAGLSFLLMAIPGALYGTSGKVSPLWLVGSWALVILGEMLISPVGLMWFLSS-------------------SVGSALNAQLFSYFGLGSVVLGIVLVFLSKRIQG-

4o6mA2

0.12

0.11

3.97

0.97

SPARKS-K

ISRLLAVTPNQITVFSFFLSLVGSALFLLNSY-------LTTLLAGVIIQLHSIIDGCDGEIARLKFMESSDFIIVFSITYVLSIGFLAAFASLMIAYTGDKYMRTYSPEGFAIPITRDFRLLIIFACSVLALVIIALLGNFEALRRIVALR

7d3uA

0.15

0.11

3.74

1.01

CNFpred

-----ATPVSAYLHAAAMVKAGIYLLLRFSEALH---VPVWNLLLITCGMTTAVLGAVFAMQRD-------DLKELLAYSTISQLGFLVATIGVGT-----------------------PAAMVAAIIHTIAHALFKSSLFMFVGVVD----

5j65A

0.05

2.38

1.17

DEthreader

-L--TISGDMTNQFIISKEWATIGAYIQTGGLYCSKTSAEWWNKNLYPLIIKSANDIASYGFGDGYRGILIEAKQYEEAAKNIVTSLDQFLHGVINIQKRLK---EVQLNGLEVKLSINTDIDNLYSQGQEAIKVFQKLQGIWATIGAQIEN

6akfA

0.13

0.12

4.11

0.92

MapAlign

MSMGLEITGTSLAVLGWLCTIVCCALLWYDSLLALPQDLQAARALIVVSILLAAFGLLVALAVQDETAKAKITIVAGVLFLLAALLTLVAVSWSANTI-------IRDFYNPLVPEAQKREMGAGLYVGWAAAALQLLGGALLAAS------

5y78A

0.09

3.24

0.61

MUSTER

VGSALGEFFHPLTYLTLVPIVSGVALSAATEL-TFTWTGFITAMISNVAFVTRNITSKFTMVDFKNEKTLIAQNTYALITIISFFMELPFALLMEG----------FPPLVSAIAGVSKAKLFGSIMFCSLFYHLYNEVSYLCLDNVSPVSF

(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	0.8445

(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	5vjsA	0.76	3.23	0.047	0.954	model1_5vjsA.pdb.gz
2	1qoyA	0.71	3.44	0.041	0.947	model1_1qoyA.pdb.gz
3	7nmqA	0.71	3.81	0.046	0.967	model1_7nmqA.pdb.gz
4	1y8pA	0.69	3.47	0.063	0.895	model1_1y8pA.pdb.gz
5	3crlB	0.69	3.12	0.056	0.868	model1_3crlB.pdb.gz
6	3d2rB	0.68	3.15	0.070	0.849	model1_3d2rB.pdb.gz
7	2q8gA	0.67	3.19	0.064	0.855	model1_2q8gA.pdb.gz
8	1gkzA1	0.65	3.14	0.069	0.836	model1_1gkzA1.pdb.gz
9	2vouA	0.38	4.77	0.034	0.599	model1_2vouA.pdb.gz
10	3t0qA	0.37	4.65	0.042	0.612	model1_3t0qA.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:0019911	0.63	structural constituent of myelin sheath
GO:0003824	0.55	catalytic 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 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	0.96	single-organism process
GO:0009987	0.96	cellular process
GO:0044763	0.92	single-organism cellular process
GO:0065007	0.90	biological regulation
GO:0051179	0.89	localization
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0051641	0.84	cellular localization
GO:0008104	0.84	protein localization
GO:0032502	0.83	developmental process
GO:0006810	0.83	transport
GO:0048518	0.79	positive regulation of biological process
GO:1902578	0.78	single-organism localization
GO:0071702	0.78	organic substance transport
GO:0065008	0.78	regulation of biological quality
GO:0048856	0.78	anatomical structure development
GO:0048522	0.78	positive regulation of cellular process
GO:0016043	0.78	cellular component organization
GO:1902580	0.77	single-organism cellular localization
GO:0048869	0.77	cellular developmental process
GO:0044767	0.77	single-organism developmental process
GO:0031579	0.77	membrane raft organization
GO:0009966	0.77	regulation of signal transduction
GO:0006886	0.77	intracellular protein transport
GO:0080090	0.76	regulation of primary metabolic process
GO:0031323	0.76	regulation of cellular metabolic process
GO:0051128	0.75	regulation of cellular component organization
GO:0032879	0.74	regulation of localization
GO:0048519	0.72	negative regulation of biological process
GO:0051239	0.71	regulation of multicellular organismal process
GO:0048523	0.71	negative regulation of cellular process
GO:0045785	0.71	positive regulation of cell adhesion
GO:0044765	0.71	single-organism transport
GO:0001932	0.71	regulation of protein phosphorylation
GO:1900026	0.70	positive regulation of substrate adhesion-dependent cell spreading
GO:0090038	0.70	negative regulation of protein kinase C signaling
GO:0072661	0.70	protein targeting to plasma membrane
GO:0061028	0.70	establishment of endothelial barrier
GO:0034115	0.70	negative regulation of heterotypic cell-cell adhesion
GO:0030837	0.70	negative regulation of actin filament polymerization
GO:0030335	0.70	positive regulation of cell migration
GO:0010629	0.70	negative regulation of gene expression
GO:0001933	0.70	negative regulation of protein phosphorylation

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:0005737	0.70	cytoplasm
GO:0044444	0.59	cytoplasmic part
GO:0043226	0.55	organelle
GO:0043229	0.53	intracellular organelle
GO:0043227	0.50	membrane-bounded 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

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	1h2rL	0.588	4.04	0.049	0.888	1.12.2.1	NA
2	0.060	1j3uA	0.592	3.92	0.050	0.895	4.3.1.1	65
3	0.060	1ivhA	0.562	4.20	0.090	0.862	1.3.99.10	126
4	0.060	1u8vA	0.616	3.94	0.055	0.921	5.3.3.3	NA
5	0.060	1jqnA	0.577	3.79	0.049	0.789	4.1.1.31	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	0.04	2zdxB	0.675	3.07	0.063	0.842	0.38	P4A	complex1.pdb.gz	10,13,17,52,76
2	0.02	2q8iA	0.676	3.19	0.056	0.862	0.21	RDC	complex2.pdb.gz	1,4,5,54
3	0.02	3d2rA	0.674	3.14	0.064	0.849	0.13	ADP	complex3.pdb.gz	72,73,75,76
4	0.02	1xly1	0.645	3.38	0.104	0.882	0.25	III	complex4.pdb.gz	42,45,48,49,51,52,55,56,63,64,69,70,79,82,85,89,92,93,96
5	0.02	1xly0	0.643	3.45	0.104	0.882	0.26	III	complex5.pdb.gz	47,48,51,52,55,56,58,61,62,73,77,82,85,86,90
6	0.01	2e0aB	0.688	3.45	0.063	0.895	0.15	ANP	complex6.pdb.gz	10,47,48,49,51,52
7	0.01	3ayxA	0.635	3.84	0.054	0.934	0.19	UUU	complex7.pdb.gz	12,53,56
8	0.01	1y8pA	0.686	3.47	0.063	0.895	0.12	ATP	complex8.pdb.gz	10,68,69,70,71,72
9	0.01	1jm6B	0.652	2.63	0.053	0.789	0.20	ADP	complex9.pdb.gz	10,13,14,60,61

	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.