D-I-TASSER A6NDP7-D1

D-I-TASSER results for A6NDP7-D1

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

Input Sequence in FASTA format

>A6NDP7 (155 residues)
MGSTMEPPGGAYLHLGAVTSPVGTARVLQLAFGCTTFSLVAHRGGFAGVQGTFCMAAWGF
CFAVSALVVACEFTRLHGCLRLSWGNFTAAFAMLATLLCATAAVLYPLYFARRECSPEPA
GCAARDFRLAASVFAGLLFLAYAVEVALTRARPGQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGSTMEPPGGAYLHLGAVTSPVGTARVLQLAFGCTTFSLVAHRGGFAGVQGTFCMAAWGFCFAVSALVVACEFTRLHGCLRLSWGNFTAAFAMLATLLCATAAVLYPLYFARRECSPEPAGCAARDFRLAASVFAGLLFLAYAVEVALTRARPGQ
Prediction	CCCCCCCCCCCSSCHHHHHCHHHHHHHHHHHHHHHHHHHHSSCCCCCCCCCCSSHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHSSCCCCC
Confidence	99998999983340034322789999999999727665311046555675767304589999999999999986454323245367428999999999999999988887631467778887312256789999999999999986202314799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGSTMEPPGGAYLHLGAVTSPVGTARVLQLAFGCTTFSLVAHRGGFAGVQGTFCMAAWGFCFAVSALVVACEFTRLHGCLRLSWGNFTAAFAMLATLLCATAAVLYPLYFARRECSPEPAGCAARDFRLAASVFAGLLFLAYAVEVALTRARPGQ
Prediction	86462665443303242133222322121132123010000233434333101000001313331330110100313430212045131000021111133123110211032334544443432422000000023013111210000224558
	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

CCCCCCCCCCCSSCHHHHHCHHHHHHHHHHHHHHHHHHHHSSCCCCCCCCCCSSHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHSSCCCCC
MGSTMEPPGGAYLHLGAVTSPVGTARVLQLAFGCTTFSLVAHRGGFAGVQGTFCMAAWGFCFAVSALVVACEFTRLHGCLRLSWGNFTAAFAMLATLLCATAAVLYPLYFARRECSPEPAGCAARDFRLAASVFAGLLFLAYAVEVALTRARPGQ

6vd7A

0.08

3.09

1.02

EigenThreader

DFLLKDPPESKYKGLRLELAVDKLVSCIAVGLPLLLISLAFAQEITLGFFPYILLLVAVLLYLPNLFWRSDLKFVMEELDKCYNRDICRVVTLIIVFTACIYLGYYISLFSGILRNDTALPPLAVGVFRLLSYINLIIYVLIMPFIIYAMLVPFR

5j65A

0.08

0.07

2.82

1.17

DEthreader

---------------TIKNSGDMTNQFIISKEWATIGAYIQTGGLYCSTSAEWWNKNLYPLIIKSANDIASYGFKGGYRGILIEAKQYEEAAKNIVTSLDQFLHGVINIQKRLKVQLIGMLNSINTDIDNLYSQGQEAIKVFQKLQGIWATIGAQ

6akfA

0.13

0.10

3.38

0.74

CEthreader

-------------------SMSMGLEITGTSLAVLGWLCTIVCCAAARALIVVSILLAAFGLLVALVGAQATNAVQD-------ETAKAKITIVAGVLFLLAALLTLVAVSWSANTIIREMGAGLYVGWAAAALQLLGGALLAAS----------

6akfA

0.10

0.08

3.13

0.78

EigenThreader

-------------SMSMGL--EITGTSLAVLGWLCTIVCCALPMWDLQAARALIVVSILLAAFGLLVALVGAQATNAVQDETAKAKITIVAGVLFLLAALLTLVAVSWSANTIIRDFYNEAQKREMGGLYVGWAAAALQLLGGALLAAS------

7lkpA3

0.08

3.04

0.66

FFAS-3D

-GPQLNTGTQL-----VLQHVQALLVLAQIVLPATFVFLALMLSIVIPTTSVDAVVAICVIFSMSFVPASFVLYLIQERVGVSPTTYWVTNFLWDIMNYSVSAGLVVGIFIGFQKKAYTSPENLPALVALLLLYGAVIPMMYPASFLFDVPST--

3rlbA

0.08

3.07

0.96

SPARKS-K

IISLIPNTVYGWIIVEIACIPILLLSLRRLTAGLVGGLIWGILSMITGHAYILSLSQAFLEYLVAPVSLGIAGLFRQKTAPLKLAPVLLGTFVAVLLKYFFHFIAGIIFWSQYAWKGWG---AVAYSLAVNGISGILTAIAAFVILIIFVKKFPK

3rkoB

0.09

0.06

2.46

1.00

CNFpred

--------------------PVSALIHAATMVTAGVYLIARTHGLFLM-TPEVLHLVGIVGAVTLLLAGFAALVQT-------DIKRVLAYSTMSQIGYMFLALGVQA---------------WDAAIFHLMTHAFFKALLFLASGSVILACHHE

5vjsA

0.04

0.03

1.77

1.17

DEthreader

---------------PELRQEHQQLAQEFQQLLQEIQQLGRELLEKHIELLETLQQTGQEAQQLLQELQQTGQELWQL-GGPELRQKHQQLAQKIQQLLQKHQQLGAKILEDEEHILLKGELQGIKQYRELQQLGQKAQQLVQKLQQTGQKLWQG

6akfA

0.14

0.12

4.20

0.97

MapAlign

------------MSMGLEI-TGTSLAVLGWLCTIVCCALWRVSAGLLPQDLQAARALIVVSILLAAFGLLVALAVQDETAKAKITIVAGVLFLLAALLTLVAVSWSANTIIRDFYNPLVPEAQKR-EMGAGLYVGWAAAALQLLGGALLAAS---

6ei3A

0.08

3.26

0.62

MUSTER

LLALACLGLTEQLGLVICLCMALVLLLAGIGGGTWWQLERARGTHPDAAVDGVRALLRVLVIFALVTPFFSLFDQKASTWVLPAWFTASQMQALNPLLVMLLIPFNNLVLYPL-LRRLGWEPTSLRRMTSGIAFSGVAWIAVGAIQVAMDGGEPM

(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	0.7992

(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	0.73	2.93	0.035	0.890	model1_5vjsA.pdb.gz
2	6grjG	0.69	3.05	0.028	0.877	model1_6grjG.pdb.gz
3	6g9lA	0.68	3.42	0.065	0.897	model1_6g9lA.pdb.gz
4	5j65A	0.68	3.17	0.021	0.897	model1_5j65A.pdb.gz
5	1y8pA	0.67	3.19	0.047	0.845	model1_1y8pA.pdb.gz
6	3crlB	0.67	3.08	0.020	0.839	model1_3crlB.pdb.gz
7	3d2rB	0.66	2.89	0.014	0.819	model1_3d2rB.pdb.gz
8	2q8gA	0.66	2.87	0.027	0.813	model1_2q8gA.pdb.gz
9	1gkzA1	0.62	3.25	0.049	0.806	model1_1gkzA1.pdb.gz
10	3d36B	0.37	4.53	0.028	0.613	model1_3d36B.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:0003824	0.65	catalytic activity
GO:0000166	0.57	nucleotide binding
GO:0035639	0.53	purine ribonucleoside triphosphate binding
GO:0032555	0.53	purine ribonucleotide binding
GO:0032550	0.53	purine ribonucleoside 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	0.97	single-organism process
GO:0009987	0.97	cellular process
GO:0044763	0.95	single-organism cellular process
GO:0065007	0.86	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0016043	0.81	cellular component organization
GO:0050794	0.80	regulation of cellular process
GO:0065008	0.76	regulation of biological quality
GO:0032502	0.71	developmental process
GO:0080090	0.70	regulation of primary metabolic process
GO:0031323	0.70	regulation of cellular metabolic process
GO:0051179	0.68	localization
GO:0048583	0.67	regulation of response to stimulus
GO:0044767	0.67	single-organism developmental process
GO:0048856	0.66	anatomical structure development
GO:0048519	0.66	negative regulation of biological process
GO:0051239	0.65	regulation of multicellular organismal process
GO:0048523	0.65	negative regulation of cellular process
GO:0006810	0.65	transport
GO:0048869	0.64	cellular developmental process
GO:0051641	0.62	cellular localization
GO:0008104	0.62	protein localization
GO:0048518	0.61	positive regulation of biological process
GO:1902578	0.60	single-organism localization
GO:0061028	0.60	establishment of endothelial barrier
GO:0071702	0.59	organic substance transport
GO:0051128	0.59	regulation of cellular component organization
GO:0048522	0.59	positive regulation of cellular process
GO:1902580	0.58	single-organism cellular localization
GO:0031579	0.58	membrane raft organization
GO:0009966	0.58	regulation of signal transduction
GO:0050896	0.57	response to stimulus
GO:0032879	0.57	regulation of localization
GO:0006886	0.57	intracellular protein transport
GO:0045785	0.55	positive regulation of cell adhesion
GO:0044765	0.55	single-organism transport
GO:0001932	0.55	regulation of protein phosphorylation
GO:1900026	0.53	positive regulation of substrate adhesion-dependent cell spreading
GO:0090038	0.53	negative regulation of protein kinase C signaling
GO:0072661	0.53	protein targeting to plasma membrane
GO:0044237	0.53	cellular metabolic process
GO:0034115	0.53	negative regulation of heterotypic cell-cell adhesion
GO:0030837	0.53	negative regulation of actin filament polymerization
GO:0030335	0.53	positive regulation of cell migration
GO:0010629	0.53	negative regulation of gene expression
GO:0001933	0.53	negative regulation of protein phosphorylation
GO:1901700	0.50	response to oxygen-containing compound
GO:0045216	0.50	cell-cell junction organization
GO:0010033	0.50	response to organic substance

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	0.73	cytoplasm
GO:0044444	0.56	cytoplasmic part
GO:0043226	0.52	organelle
GO:0043229	0.50	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

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	1y0vD	0.559	3.95	0.061	0.793	4.6.1.1	30,146
2	0.060	2frvD	0.605	3.77	0.066	0.890	1.12.2.1	NA
3	0.060	2wpnB	0.607	3.42	0.062	0.800	1.12.7.2	137
4	0.060	1h0nA	0.553	4.45	0.077	0.871	1.17.4.1	NA
5	0.060	1vdkA	0.557	4.02	0.039	0.832	4.2.1.2	101

	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	0.03	2q8gA	0.658	2.87	0.027	0.813	0.58	AZX	complex1.pdb.gz	24,25,28,29,138,141
2	0.02	1y8oA	0.667	2.98	0.054	0.832	0.60	RED	complex2.pdb.gz	29,32,59
3	0.02	2w6dA	0.632	3.32	0.042	0.852	0.71	GDP	complex3.pdb.gz	32,33,35,58
4	0.01	3tj6A	0.483	3.89	0.042	0.690	0.50	III	complex4.pdb.gz	25,28,32,35,36,39,55,86,92,96,103
5	0.01	2gdcA	0.455	3.67	0.035	0.652	0.53	III	complex5.pdb.gz	21,24,25,28,29,32,35,54,85,92,96,99,100,103
6	0.01	2ibfA	0.447	3.96	0.035	0.658	0.57	III	complex6.pdb.gz	23,24,26,27,29,33,36,37,59
7	0.01	3s90A	0.455	3.81	0.035	0.658	0.51	III	complex7.pdb.gz	21,22,26,29,30,33,36,54,95,99,102,103,106

	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.