D-I-TASSER Q5VYM1-D2

D-I-TASSER results for Q5VYM1-D2

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

Input Sequence in FASTA format

>Q5VYM1 (187 residues)
KMVSQVPSQGPCVHMEAGVDYLSPGPGEPSNSKVLVSGKRKDKASASSSAKKREHPRKPK
AGDHRRGTARLGLSTVTGKNHPAQARSLVEAPVSTFPQRSQHRGQSSQHTALPQLLLPKA
SGPQDQPEAGRRASDILTPRHCKHCPWAHMEKYLSFPTLKASLTRGLQKVLAKCLDNHRP
LPTKSSQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| KMVSQVPSQGPCVHMEAGVDYLSPGPGEPSNSKVLVSGKRKDKASASSSAKKREHPRKPKAGDHRRGTARLGLSTVTGKNHPAQARSLVEAPVSTFPQRSQHRGQSSQHTALPQLLLPKASGPQDQPEAGRRASDILTPRHCKHCPWAHMEKYLSFPTLKASLTRGLQKVLAKCLDNHRPLPTKSSQ
Prediction	CCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCC
Confidence	9754346765136642245567877678999878899866666668762113778999997545888788788877788881442360237677789974123799985557632276778987786677777777787556677552512138999999985226899999996347888887789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| KMVSQVPSQGPCVHMEAGVDYLSPGPGEPSNSKVLVSGKRKDKASASSSAKKREHPRKPKAGDHRRGTARLGLSTVTGKNHPAQARSLVEAPVSTFPQRSQHRGQSSQHTALPQLLLPKASGPQDQPEAGRRASDILTPRHCKHCPWAHMEKYLSFPTLKASLTRGLQKVLAKCLDNHRPLPTKSSQ
Prediction	8335416442221223454544455274344362454445555541343354475365354563563545233344456535544441573446433643554755354343245424644447446745456753543441441323434641554446344343144003301443442446678
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCC
KMVSQVPSQGPCVHMEAGVDYLSPGPGEPSNSKVLVSGKRKDKASASSSAKKREHPRKPKAGDHRRGTARLGLSTVTGKNHPAQARSLVEAPVSTFPQRSQHRGQSSQHTALPQLLLPKASGPQDQPEAGRRASDILTPRHCKHCPWAHMEKYLSFPTLKASLTRGLQKVLAKCLDNHRPLPTKSSQ

2cf2C

0.05

2.26

0.56

CEthreader

GGEGKGRALGVGEVKFTGQVLPTAKKVTYRIHFKRIVNRRLIMGLADGEV-------LVDGRLIYTASDLKVGLFQDTSAFVDKRESYTKEDLLASGRGELFGAKGPQLPAPNMLMMDRVVKMTETGGNFDKGYVEAELDINPDLWFFGCHFIGDPVMPGCLGLDAMWQLVGFYLGWLGGEGKGRAL

1e6dM

0.03

1.66

0.60

EigenThreader

LSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFS---------LEPPAPEYGLSFAAPLKEGGLFLIASFFMFVAVWSWWGRTYLRAQALTNNFSLVHG---NLRYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGDRGTAAERAALFWRWTMGFNWMAVLVTLTGGIGILLSGTVVDNWYV

2akhY

0.11

3.82

0.39

FFAS-3D

--IGNGISIIIFAGIVAGLPPAIAHTIEQARQGDLHFLVERGQRRIVVNYAKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSASWFGGGTGWNWLTTISLYLQPGQALVFNPRETADNLKKSGAFVPGIRPGEQTAK---------YIDKVMTRLTLVGALYITFICLIPEFMRDAMKVPFYFG-

6emkG

0.07

0.06

2.39

1.27

SPARKS-K

YASYHGRYLICVYLIQLGHDKHELIKTFKGNTCVHLALMKGHEQTLHLLLQQFPRFI--NHRGENGRAP-IHIACMNDYYQCLSLLIGVGADLWVMD----TNGDTPLHVCLEYG-SISCMKMLLNEGDNVRDKGNWKPIDVQTFEVGNIYSKVLKEV-----------------------------

4tmuA

0.14

0.03

1.10

0.23

CNFpred

------------------------------------------------------------------------------------------------------------------------------------------QAPCGNCDICL------DPPRRYDGLVDAQKALSAIARVEQRFGMGYVV

1dgjA

0.03

0.02

1.41

0.83

DEthreader

------VNGMARLVLRKVGCGKG--QCGACT---------------VILDGKVVRAIIKMS-RVAENASVTTGIGHPLQHWIQHGAAQCCTG-HPKSVAIHLH----GF-FRGYGAP-EEFRCY-TSQPEYGAGLDGPDTSEANSWAGSGQGRKICNKVVDGQIYGGLAQGVGEGPSMIPDDIEIVY

3jcrD

0.05

0.04

1.76

0.89

MapAlign

--CTGSDDGTVKLW--------------------------------------------DIRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTGLSLSGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFKNLLRCSWSPDGSKIAAGSADRFVYVWDTTSRR

6fmlG

0.11

3.89

0.87

MUSTER

DLFERADTSSPCGHFAETGSFLREGVALGYSTRSLVEYRLPRLIWCDGGRLDKPGPGNLVAGFRSKYLNHMMNIWTPESSLEGIENFTWLRFVDTSLQEAYRASHTDVFARAVDLASKQNRLGHMQIVYDEPEDKKWTPVHALFQICERENPKAVAEITTEGVLRDLMNIARVKYRELGLCRLEKAA

1vt4I3

0.13

0.08

2.79

0.64

HHsearch

---------------------------EYALHRSIVDH----YNIP--KTFDSDDLIPPYLDQY------F-------YSHIGHHLNIEHPERMTLF------RMVF---LDFRFLEQKIRHDSTAWNA---SGSILKFYKPYICDNDPK------------YERLVNAILDFLPKIEENL-ICSKY

3smaA

0.05

2.44

0.51

CEthreader

GKEGTLVMPTFSGDLSDPSTWRRPPVPEDWWPVIREQMPPFDPDLTPTRGMGAVARRAAGAVRSGHPQNSFAAWGAHAEQVVAEHGLTERLGRGSPLEQVYRLDGQVLLLGCGFESNTSFHLAEYRTAYPGRRSHRRRVPVPEG-DRVRWVEQEDIVYFEEDFQTMGESCLTRTPGHSRGTVGEAAA

(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	0.4492

(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	2vdcA1	0.44	5.42	0.035	0.759	model1_2vdcA1.pdb.gz
2	3hmjA	0.43	5.27	0.048	0.738	model1_3hmjA.pdb.gz
3	2y8nA	0.43	6.03	0.049	0.834	model1_2y8nA.pdb.gz
4	4tl2A1	0.43	5.28	0.047	0.738	model1_4tl2A1.pdb.gz
5	4ewgA	0.43	5.25	0.031	0.722	model1_4ewgA.pdb.gz
6	3ffzA	0.43	5.44	0.042	0.749	model1_3ffzA.pdb.gz
7	7kq3A	0.43	5.74	0.047	0.797	model1_7kq3A.pdb.gz
8	7c6oA	0.43	5.53	0.045	0.754	model1_7c6oA.pdb.gz
9	5ganC2	0.43	5.36	0.044	0.738	model1_5ganC2.pdb.gz
10	1ogyA	0.43	5.62	0.063	0.754	model1_1ogyA.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:0046872	0.86	metal ion binding
GO:0005543	0.86	phospholipid binding
GO:0005544	0.85	calcium-dependent phospholipid binding
GO:0005522	0.85	profilin binding
GO:0005509	0.85	calcium ion 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:0044699	0.89	single-organism process
GO:0044763	0.88	single-organism cellular process
GO:0006996	0.85	organelle organization
GO:0006810	0.85	transport
GO:0065007	0.78	biological regulation
GO:0050789	0.78	regulation of biological process
GO:0007165	0.68	signal transduction
GO:0035418	0.53	protein localization to synapse
GO:0030073	0.53	insulin secretion
GO:0019933	0.53	cAMP-mediated signaling
GO:0017157	0.53	regulation of exocytosis
GO:0016080	0.53	synaptic vesicle targeting
GO:0007010	0.53	cytoskeleton organization

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:0044464	1.00	cell part
GO:0044424	0.96	intracellular part
GO:0043229	0.79	intracellular organelle
GO:0043227	0.79	membrane-bounded organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0005634	0.56	nucleus
GO:0044444	0.52	cytoplasmic part
GO:0016020	0.50	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	2iirJ	0.410	5.43	0.042	0.733	2.7.2.1	NA
2	0.060	1ig8A	0.432	5.76	0.029	0.791	2.7.1.1	NA
3	0.060	1f1uA	0.411	5.36	0.069	0.711	1.13.11.15	NA
4	0.060	3ffzA	0.429	5.44	0.042	0.749	3.4.24.69	NA
5	0.060	1afwB	0.406	5.17	0.033	0.684	2.3.1.16	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	2nyaA	0.428	5.74	0.087	0.765	0.43	SF4	complex1.pdb.gz	12,14,15,17,62,66,67
2	0.01	1lm1A	0.428	5.91	0.074	0.797	0.58	F3S	complex2.pdb.gz	15,16,17,58,59,62,66
3	0.01	1llzA	0.402	5.57	0.047	0.706	0.42	F3S	complex3.pdb.gz	64,65,68,69,70,71
4	0.01	1ogyA	0.428	5.62	0.063	0.754	0.44	SF4	complex4.pdb.gz	14,18,63,66,67
5	0.01	3fahA	0.412	6.33	0.050	0.840	0.59	GOL	complex5.pdb.gz	67,68,70,72

	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.