D-I-TASSER Q8NEQ6-D1

D-I-TASSER results for Q8NEQ6-D1

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

Input Sequence in FASTA format

>Q8NEQ6 (169 residues)
MAPSEDPRDWRANLKGTIRETGLETSSGGKLAGHQKTVPTAHLTFVIDCTHGKQLSLAAT
ASPPQAPSPNRGLVTPPMKTYIVFCGENWPHLTRVTPMGGGCLAQARATLPLCRGSVASA
SFPVSPLCPQEVPEAKGKPVKAAPVRSSTWGTVKDSLKALSSCVCGQAD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MAPSEDPRDWRANLKGTIRETGLETSSGGKLAGHQKTVPTAHLTFVIDCTHGKQLSLAATASPPQAPSPNRGLVTPPMKTYIVFCGENWPHLTRVTPMGGGCLAQARATLPLCRGSVASASFPVSPLCPQEVPEAKGKPVKAAPVRSSTWGTVKDSLKALSSCVCGQAD
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCC
Confidence	9877787451116676766777531799885666778876414666403678755667899999999999898599875225632788999766677898854446788999888888887898998865587667886666765578753124568887764214579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MAPSEDPRDWRANLKGTIRETGLETSSGGKLAGHQKTVPTAHLTFVIDCTHGKQLSLAATASPPQAPSPNRGLVTPPMKTYIVFCGENWPHLTRVTPMGGGCLAQARATLPLCRGSVASASFPVSPLCPQEVPEAKGKPVKAAPVRSSTWGTVKDSLKALSSCVCGQAD
Prediction	8545744653444255344445154345544544563333230211022244551434345434745555633334424330310274435444634254431643744343344444644244535334742646645154345444534413431521321223448
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCC
MAPSEDPRDWRANLKGTIRETGLETSSGGKLAGHQKTVPTAHLTFVIDCTHGKQLSLAATASPPQAPSPNRGLVTPPMKTYIVFCGENWPHLTRVTPMGGGCLAQARATLPLCRGSVASASFPVSPLCPQEVPEAKGKPVKAAPVRSSTWGTVKDSLKALSSCVCGQAD

3ei2A3

0.09

3.40

0.43

CEthreader

LTYLDNGVVFVGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLEGQLVTCSGAFKEGSLRIIIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGK

4ksrA

0.07

2.70

0.52

EigenThreader

EKTPSRKLSSLLVSRVKVMAKLDIAEKRVMPSSHGEIKRPHGIILVTGPTGSGKSTTLYAGLQELNSPIEFDIDGIGHLVMSTLH-------TNTAVGAVTRLRDMGIEPDCKEPLRATGCPKCNHKGDDALQELIHSEAGEQAMEKHIRATTPNLMMACSSG---KHY

5y7oA1

0.16

0.14

4.72

0.35

FFAS-3D

-----DWRDEVEGGDVIIWLNDLTKDKRGQLPAVRRDV--HNVVIPIDLTNEDDVYVVQ-------HIQTFIKRLIPVRFGLVPLVHSEPEKDKLARPDQALFDETIASARVLRGKAQSFEEALSSTTLEEVDKTNGVLLGRGDNFLQELSRVAIDLQLIQQSI-----

5aftV

0.09

3.36

0.90

SPARKS-K

-----SGNKVSRQSVLCGSQ-NIVLNGKTIIMNDCIIRGLANVRVGRHCVVKSRSVIRPPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRCVLKDCCKILDNTVLPPETVVPPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFLPLTQ

3h2gA

0.12

0.03

1.05

0.41

CNFpred

----------------------------------------AEFTYATIGVEGEPATASGVLLIPGGERCSG-----PYPLLGWGHPT----------------------------------------------------------------------------------

6ak1A

0.07

0.05

2.01

0.83

DEthreader

---------DVVGVYAEALRADVPVNDPTAAVVAQAGFIL-T---------------TSVQAITIRQARSDSIKIFMLLTVITAEAK-QEYLSYA--N-PEGMLLYGWTLRTTESLTHVRERCIGGLGP---------------YA--VTPGSVTDFIDYIVPELRKRG

4xnnA

0.08

3.07

0.84

MapAlign

-LCPTPETCTTNCPLADWSGTYGGSVTGNKFNLKYYGNCCAELDIWEANKQSQAFTTHPCGVVCGDNDSGDRYNGMCDKDGCDFASYRMNDHTFYGPGSTFKLDSTKPFTVVSQFITTDGTDNGDFKEFRRFYVQNGVRIGITAYDSITDEMCAATKGLFLDDHKNKGG

4k0mC

0.12

0.11

3.98

0.69

MUSTER

IDPRRSDQNVRGTVSGLGKQVRVLAIAKGEKIKEAEEAGADYVG----GEEIIQAAAAAAAAAAAAAAAAAAAAAAAAA------AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

2pffB

0.19

0.18

5.90

0.51

HHsearch

ENPSNTPDKYLLSAKLLELRSYLKGATGSFFVSVRKAI---TVLFFIGVRCYEAYPNTSLPPSIEDSLENNEGVPSPMLSYVNKTN---SHLPAGKQVEISLVNGAKNLVPPLRKAKAPSGLPFSEFSNRFLPVASPFHSLLVP---ASDLINKDLVKNNVSPVYDTFD

4asmB

0.07

2.76

0.41

CEthreader

TFNPTNNVVDFGPNGNMKWYNKYHNRPNGQPNNFEGPGPTKWMQNHVAVSGGNLNIWASRIATKSFTGSNNTPISRPETRAGCITNKTRVMNSTLASDIWLLSPDDTQCYGGPGNDNRNSYFASKIHLSHHVFIRPPNFKDYQPADLNSWWGKNGVTQWGGKTIRIGVN

(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	0.4771

(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	2cwnA	0.46	5.23	0.054	0.787	model1_2cwnA.pdb.gz
2	3m16A	0.45	5.14	0.060	0.787	model1_3m16A.pdb.gz
3	1i2rA	0.45	5.30	0.040	0.799	model1_1i2rA.pdb.gz
4	3cq0A	0.45	5.41	0.082	0.817	model1_3cq0A.pdb.gz
5	6wy8B	0.44	4.96	0.059	0.722	model1_6wy8B.pdb.gz
6	6snhX	0.43	5.32	0.061	0.757	model1_6snhX.pdb.gz
7	2jbsC	0.43	5.00	0.046	0.740	model1_2jbsC.pdb.gz
8	1jroB	0.43	5.77	0.025	0.823	model1_1jroB.pdb.gz
9	5mq6A	0.43	5.34	0.069	0.775	model1_5mq6A.pdb.gz
10	1jqoA	0.43	5.33	0.046	0.775	model1_1jqoA.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:0008092	0.72	cytoskeletal protein binding
GO:0032403	0.69	protein complex binding
GO:0003824	0.65	catalytic activity
GO:0016740	0.64	transferase activity
GO:0005198	0.63	structural molecule activity
GO:0097493	0.62	structural molecule activity conferring elasticity
GO:0051371	0.62	muscle alpha-actinin binding
GO:0051015	0.62	actin filament binding
GO:0008307	0.62	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	0.93	cellular process
GO:0044699	0.91	single-organism process
GO:0044763	0.89	single-organism cellular process
GO:0022607	0.79	cellular component assembly
GO:0034622	0.73	cellular macromolecular complex assembly
GO:0006461	0.73	protein complex assembly
GO:0044767	0.72	single-organism developmental process
GO:1902589	0.71	single-organism organelle organization
GO:0070925	0.71	organelle assembly
GO:0032501	0.71	multicellular organismal process
GO:0010927	0.71	cellular component assembly involved in morphogenesis
GO:0048856	0.67	anatomical structure development
GO:0055008	0.66	cardiac muscle tissue morphogenesis
GO:0055003	0.66	cardiac myofibril assembly
GO:0048739	0.66	cardiac muscle fiber development
GO:0045214	0.66	sarcomere organization
GO:0030241	0.66	skeletal muscle myosin thick filament assembly
GO:0030240	0.66	skeletal muscle thin filament assembly
GO:0008152	0.66	metabolic process
GO:0006941	0.66	striated muscle contraction
GO:0071704	0.63	organic substance metabolic process
GO:0044237	0.61	cellular metabolic process
GO:0044238	0.59	primary metabolic process
GO:0044710	0.58	single-organism metabolic process
GO:0006807	0.57	nitrogen compound metabolic process
GO:0044281	0.56	small molecule metabolic process
GO:0006139	0.55	nucleobase-containing compound metabolic process
GO:1901135	0.54	carbohydrate derivative metabolic process
GO:0009117	0.51	nucleotide metabolic process
GO:1901564	0.50	organonitrogen compound 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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0005737	0.88	cytoplasm
GO:0044446	0.80	intracellular organelle part
GO:0044444	0.77	cytoplasmic part
GO:0044430	0.75	cytoskeletal part
GO:0043234	0.73	protein complex
GO:0031430	0.66	M band
GO:0030018	0.66	Z disc
GO:0005865	0.66	striated muscle thin filament
GO:0005859	0.66	muscle myosin complex

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	3ge1A	0.424	5.25	0.036	0.728	2.7.1.30	NA
2	0.060	3dz1A	0.410	5.26	0.049	0.698	4.2.1.52	44,83,112
3	0.060	1xdmB	0.374	5.71	0.059	0.704	4.1.2.13	NA
4	0.060	1rx0A	0.417	5.13	0.051	0.710	1.3.99.-	NA
5	0.060	1f05A	0.457	5.56	0.053	0.846	2.2.1.2	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	2w3sH	0.423	5.78	0.039	0.823	0.14	XAN	complex1.pdb.gz	49,85,86
2	0.01	2w3sD	0.422	5.97	0.026	0.834	0.13	MPN	complex2.pdb.gz	55,56,85
3	0.01	1cvuB	0.429	5.75	0.052	0.793	0.11	ACD	complex3.pdb.gz	83,87,118,148,156,157
4	0.01	2w3sF	0.423	5.84	0.040	0.817	0.20	XAN	complex4.pdb.gz	45,48,52
5	0.01	3hs5B	0.429	5.74	0.039	0.793	0.11	ACD	complex5.pdb.gz	85,86,150,154,156,157,160
6	0.01	2w3sB	0.420	5.84	0.039	0.834	0.13	XAN	complex6.pdb.gz	50,51,88
7	0.01	1jroF	0.435	5.64	0.043	0.823	0.10	UUU	complex7.pdb.gz	16,19,20
8	0.01	3hs7A	0.430	5.80	0.039	0.799	0.12	COH	complex8.pdb.gz	56,58,153
9	0.01	2w3rB	0.432	5.89	0.043	0.864	0.13	HPA	complex9.pdb.gz	50,51,86,87
10	0.01	2w3rF	0.436	5.71	0.043	0.834	0.25	UUU	complex10.pdb.gz	85,86,104,105,106

	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, 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.