D-I-TASSER Q5VTL7-D8

D-I-TASSER results for Q5VTL7-D8

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

Input Sequence in FASTA format

>Q5VTL7 (104 residues)
CPLGVKLYRLGPNGIRIYWQASRGSANYSTDLYGSKGIFTCTPSAGLSFCDVTEIPCGDV
YTVMVSPVAKTGLKLTFCPKKIYSVTCSGSTLGMVIYRGKRNEE

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| CPLGVKLYRLGPNGIRIYWQASRGSANYSTDLYGSKGIFTCTPSAGLSFCDVTEIPCGDVYTVMVSPVAKTGLKLTFCPKKIYSVTCSGSTLGMVIYRGKRNEE
Prediction	CCCCCSSSSSCCCCSSSSSSSCCCCCSSSSSSSSCCCCSSSCCCCCCCSCCSSSSCCCCSSSSSSSSSCCCCCSSSSCCCCSSSSSCCCCCSSSSSSSCCCCCC
Confidence	99765799836980699996079840279999926763455566787321012111674799999872168946875277507787189844789993344689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| CPLGVKLYRLGPNGIRIYWQASRGSANYSTDLYGSKGIFTCTPSAGLSFCDVTEIPCGDVYTVMVSPVAKTGLKLTFCPKKIYSVTCSGSTLGMVIYRGKRNEE
Prediction	55561413424643030204447433423130334434241344343420413413234312010321467544241125422313034431010012245578
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCSSSSSCCCCSSSSSSSCCCCCSSSSSSSSCCCCSSSCCCCCCCSCCSSSSCCCCSSSSSSSSSCCCCCSSSSCCCCSSSSSCCCCCSSSSSSSCCCCCC
CPLGVKLYRLGPNGIRIYWQASRGSANYSTDLYGSKGIFTCTPSAGLSFCDVTEIPCGDVYTVMVSPVAKTGLKLTFCPKKIYSVTCSGSTLGMVIYRGKRNEE

6mfaA

0.10

3.57

1.33

DEthreader

APTNLQFVNETDSTVLVRWTPPRQITGYRLTVGLGPRQYNVGP-S-VSKYPLRNLQPASEYTVSLVAIKGNQESPKA-TGVFTTLQPGSSIPPYNTEVIVVTPL

3teuA

0.13

0.12

3.99

1.31

SPARKS-K

APTDLQVTNVTDTSITVSWTPPSAITGYRITYTPSNGPKELTVPPSSTSVTITGLTPGVEYVVSVYALKDNQESPPLVGTQTTGGHHHHHH-------------

1wfnA

0.13

0.11

3.66

0.34

MapAlign

PVGHLSFSEILDTSLKVSWQEPGILTGYRISWEEYRVTHYLPN--VTLEYRVTGLTALTTYTIEVAAMTSKGQGQVS-ASTISSGVP-----------------

4wtxA

0.15

0.12

4.19

0.25

CEthreader

APGPLVFTALSPDSLQLSWERPRRIVGYLVTCEMAQTAFRVDGDSPESRLTVPGLSENVPYKFKVQARTTEGFGPER-EGIITIES------------------

4lsdA

0.13

0.12

3.97

1.12

MUSTER

APVNVTVRHLKANSAVVSWDVLEVVIGFAISQQKKDVRFIQEVNTTTRSCALWDLEEDTEYIVHVQAISIQGQSPASEPVLFKTPREAE---------------

6rpxA

0.15

0.14

4.86

0.85

HHsearch

PPVQIEELIEKPGGIIVRWCKDDFAQDYRLQFRKCTAHFEYVGSE--TEFIVLHIDPNVDYQFRVCA-RGDGRQEWSPWSVPQTGHSTGF-EGYSLSSAPTYFC

3teuA

0.16

0.13

4.49

1.17

FFAS-3D

-PTDLQVTNVTDTSITVSWTPPSAITGYRITYTPSNGPKELTVPPSSTSVTITGLTPGVEYVVSVYALKDNQESPPLV--------------GTQTTGGHHHHH

6bt9A2

0.12

4.06

0.48

EigenThreader

PTNVIVVTNKNSNSVQLNWTASTDVTEYEITAG--EEKWSTTT----NSITIKNLKPNTEYTFSIIAKDAAGNKSQPTALTVKTDENGTTPISKTNNNAGWNGE

4u3hA

0.14

0.11

3.63

1.24

CNFpred

PPGNLRVTDVTSTSVTLSWEPPPPITGYRVEYREEWKEVTVPG--SETSYTVTGLKPGTEYEFRVRAVNGAGEGPPS-SVSVTT--------------------

2uvfA

0.12

4.06

1.17

DEthreader

APQQLQVPAYDESSIVLVWKAPDTIVDYQIFSA--GKLLGKASKIVMQNFTVIGLKPETSYQFTVKAQYADSLSVASKPITAKTSAKPGCMTRYNVVNG-W---

(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	0.7779

(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	6mfaA	0.79	2.41	0.099	0.952	model1_6mfaA.pdb.gz
2	1tdqA	0.78	1.81	0.134	0.865	model1_1tdqA.pdb.gz
3	4lsdA	0.77	1.48	0.125	0.846	model1_4lsdA.pdb.gz
4	1x5hA	0.76	1.55	0.120	0.856	model1_1x5hA.pdb.gz
5	2jllA	0.76	1.75	0.127	0.856	model1_2jllA.pdb.gz
6	2vkxE	0.76	1.77	0.058	0.865	model1_2vkxE.pdb.gz
7	2ee2A	0.76	1.49	0.132	0.837	model1_2ee2A.pdb.gz
8	1qr4A	0.75	1.71	0.115	0.846	model1_1qr4A.pdb.gz
9	1va9A	0.75	1.94	0.163	0.875	model1_1va9A.pdb.gz
10	4pbxA	0.75	2.17	0.137	0.885	model1_4pbxA.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:0044877	0.85	macromolecular complex binding
GO:0032403	0.84	protein complex binding
GO:0097493	0.80	structural molecule activity conferring elasticity
GO:0051371	0.80	muscle alpha-actinin binding
GO:0051015	0.80	actin filament binding
GO:0008307	0.80	structural constituent of muscle

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	0.94	cellular process
GO:0044763	0.92	single-organism cellular process
GO:0016043	0.89	cellular component organization
GO:0048856	0.88	anatomical structure development
GO:0044767	0.88	single-organism developmental process
GO:0022607	0.88	cellular component assembly
GO:0048468	0.87	cell development
GO:0055008	0.80	cardiac muscle tissue morphogenesis
GO:0055003	0.80	cardiac myofibril assembly
GO:0048739	0.80	cardiac muscle fiber development
GO:0045214	0.80	sarcomere organization
GO:0030241	0.80	skeletal muscle myosin thick filament assembly
GO:0030240	0.80	skeletal muscle thin filament assembly
GO:0006941	0.80	striated muscle contraction
GO:0065007	0.56	biological regulation
GO:0050789	0.56	regulation of biological process
GO:0050794	0.51	regulation of cellular 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:0044464	0.99	cell part
GO:0044424	0.96	intracellular part
GO:0044444	0.93	cytoplasmic part
GO:0043234	0.92	protein complex
GO:0044446	0.91	intracellular organelle part
GO:0044421	0.84	extracellular region part
GO:0044430	0.82	cytoskeletal part
GO:0043226	0.82	organelle
GO:0031430	0.81	M band
GO:0030018	0.81	Z disc
GO:0005865	0.81	striated muscle thin filament
GO:0005859	0.81	muscle myosin complex
GO:0043227	0.78	membrane-bounded organelle
GO:0070062	0.68	extracellular exosome
GO:0005576	0.68	extracellular region
GO:0016020	0.67	membrane
GO:0043229	0.66	intracellular organelle
GO:0044425	0.61	membrane part
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0031012	0.59	extracellular matrix
GO:0005615	0.55	extracellular space
GO:0044459	0.54	plasma membrane part
GO:0005578	0.51	proteinaceous extracellular matrix

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	0.124	1k85A	0.673	1.79	0.127	0.760	3.2.1.14	22
2	0.099	2dleA	0.707	1.62	0.112	0.808	3.1.3.48	NA
3	0.088	2dlhA	0.726	2.06	0.122	0.837	3.1.3.48	NA
4	0.067	2edtA	0.581	2.66	0.047	0.779	2.7.11.1	34,65
5	0.067	2edrA	0.578	2.67	0.035	0.779	2.7.11.1	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	0.04	1tdq0	0.777	1.81	0.134	0.865	0.74	III	complex1.pdb.gz	37,59,60,62,76,79,80,81,83
2	0.02	1y6m1	0.645	2.07	0.112	0.769	0.42	III	complex2.pdb.gz	34,36,60,63,79,80,81
3	0.01	2rd58	0.332	4.56	0.036	0.577	0.44	III	complex3.pdb.gz	32,33,34,36,37,38

	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.