D-I-TASSER Q8WU10-D2

D-I-TASSER results for Q8WU10-D2

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

Input Sequence in FASTA format

>Q8WU10 (129 residues)
AKPKLICEGNPYVLGIRDTDSAQEFQKQLTKAKRIMIIGNGGIALELVYEIEGCEVIWAI
KDKIHLETMCEVKKIYLQDEFRILKKKSFTFPRDHKSVTADTEMWPVYVELTNEKIYGCD
FIVSATGVT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| AKPKLICEGNPYVLGIRDTDSAQEFQKQLTKAKRIMIIGNGGIALELVYEIEGCEVIWAIKDKIHLETMCEVKKIYLQDEFRILKKKSFTFPRDHKSVTADTEMWPVYVELTNEKIYGCDFIVSATGVT
Prediction	CCCCCCCCCCCCSSSSCCHHHHHHHHHHHHCCCSSSSSCCCHHHHHHHHHHCCCSSSSSSSCCCCCCCCCCHHHHHHHHHHHHHCCCCSSCCCCSSSSSSCCCCCSSSSSSCCCCSSCCCSSSSCCCCC
Confidence	999877899995899568899999999973297699988972689999984397499998157433234798999988999986096233252035676058885589991899885598999833539
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| AKPKLICEGNPYVLGIRDTDSAQEFQKQLTKAKRIMIIGNGGIALELVYEIEGCEVIWAIKDKIHLETMCEVKKIYLQDEFRILKKKSFTFPRDHKSVTADTEMWPVYVELTNEKIYGCDFIVSATGVT
Prediction	852624567352000012262054037306504300001233113300441561401000345422433244522432453355654544244434414467763313040553641302000002428
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCSSSSCCHHHHHHHHHHHHCCCSSSSSCCCHHHHHHHHHHCCCSSSSSSSCCCCCCCCCCHHHHHHHHHHHHHCCCCSSCCCCSSSSSSCCCCCSSSSSSCCCCSSCCCSSSSCCCCC
AKPKLICEGNPYVLGIRDTDSAQEFQKQLTKAKRIMIIGNGGIALELVYEIEGCEVIWAIKDKIHLETMCEVKKIYLQDEFRILKKKSFTFPRDHKSVTADTEMWPVYVELTNEKIYGCDFIVSATGVT

3fg2P

0.20

0.19

6.21

1.33

DEthreader

ARNRMLNASLPDVLYLRTLDESEVLRQRMPDKKHVVVIGAGFIGLEFAATARGLEVDVVELAPRMARVVTEISSYFHDR-HSGAG-IRMHY-GVRATEIAAEGDRVTGVVLSDGNTLPCDLVVVGVGVI

5er0A3

0.18

0.17

5.55

1.64

SPARKS-K

-WPIVPGIDSDRVKLCKNWAHAQALIEDAKEAKRITVIGAGYIGAELAEAYSGHDVTLIDAMAMPKYFDADFTDVIEQDYRDH-GVQ--LALGETVESFTDSAT-GLTIKTDKNS-YETDLAILCIGF-

5jciA

0.17

0.16

5.38

0.45

MapAlign

SSVIKLSADSNNILYLREVDDADKLVAAIQAKGKAVIVGGGYIGLELSAALKIFDVTMVFPEPMPRLFTADIAAFY-ESYYTNK-GVKIVKGTVAVGFDADANGDVTAVNLKNGSVLEADIVVVGVGGR

1gv4A3

0.17

0.16

5.34

0.33

CEthreader

--PRSLSAIKSRTTLFRKIGDFRALEKISREVKSITVIGGGFLGSELACALGRIEVIQLFPEKNMGKILPQYLSNWTMEKVKREGVKVMPNAIVQSVGVS---GGRLLIKLKDGRKVETDHIVTAVG--

3fg2P3

0.18

5.78

1.61

MUSTER

RMLDVPNASLPDVLYLRTLDESEVLRQRMPDKKHVVVIGAGFIGLEFAATARALEVDVVELAPRVMAVVTPEISSYFHDRHSGAGI-RMHY-GVRATEIAAEGDRVTGVVLSDGNTLPCDLVVVGVG--

6pfzD

0.20

0.19

5.98

0.73

HHsearch

ARPAIEGIEAEGVVTLTSAEEAEKIIEMWEEAEKAVVIGAGFIGLESAEALKDMEVTVIEMMDVAPMLDREMAVLVEN-HLREKGVN-VVT-STRVEKIVSQ--KVRAVI-ANGKEYPADVVVVATGIK

3ef6A3

0.16

5.17

1.52

FFAS-3D

RTMALPGSQLPGVVTLRTYGDVQVLRDSWTSATRLLIVGGGLIGCEVATTARKLGLSVTILEAGDELLVRVLGRRIGAWLRGLLTELGVQVELGTGVVGFSGEGQLEQVMASDGRSFVADSALICVG--

7jvkA2

0.15

4.96

0.73

EigenThreader

GTAKMPSGLPPRIIHS--SKYCTTLPALLSKPYNIAVLGSGQSAAEIQKRYPNSRTTLIMRDSAMSVVRLELIEEIYNDMYLQRWQHRILPERKITRVEHHGPQSRMRIHLKVKETLEVDALMVATGYN

2cduA

0.17

0.16

5.36

1.44

CNFpred

TVPPIPGIDSSRVYLCKNYNDAKKLFEEAPKAKTITIIGSGYIGAELAEAYSNYNVNLIDGHERVLYFDKEFTDILA-KDYEAHGVNLVLG--SKVAAFEEV-DDEIITKTLDGKEIKSDIAILCIGFR

5odcA

0.14

0.13

4.51

1.33

DEthreader

YDADPTYGVYDNVVTALEERMINTGKVIRQKPKRIAFIQCCMYAMKNSQLIKPTEIDIYY-MDIRA-FSKGYEEFYE-RSAKQYGI-KFM-R-GRPSQVIEDPTGNLVVRAEEILEKEYDLVVLSVGMV

(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	0.8685

(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	3fg2P	0.90	1.32	0.198	0.977	model1_3fg2P.pdb.gz
2	5jciA	0.88	1.46	0.151	0.977	model1_5jciA.pdb.gz
3	3ef6A	0.87	1.54	0.144	0.969	model1_3ef6A.pdb.gz
4	1q1wA	0.87	1.72	0.159	0.977	model1_1q1wA.pdb.gz
5	2bc0A	0.87	1.48	0.161	0.961	model1_2bc0A.pdb.gz
6	1nhqA3	0.86	1.52	0.153	0.961	model1_1nhqA3.pdb.gz
7	2cduA	0.85	1.75	0.168	0.969	model1_2cduA.pdb.gz
8	5er0A	0.85	1.80	0.185	0.961	model1_5er0A.pdb.gz
9	3kd9A	0.85	1.65	0.171	0.954	model1_3kd9A.pdb.gz
10	3lxdA	0.85	1.82	0.167	0.977	model1_3lxdA.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:0050660	0.82	flavin adenine dinucleotide binding
GO:0016491	0.64	oxidoreductase activity
GO:0016651	0.54	oxidoreductase activity, acting on NAD(P)H
GO:0016667	0.52	oxidoreductase activity, acting on a sulfur group of donors
GO:0016620	0.52	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0016668	0.51	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:1901681	0.50	sulfur compound binding
GO:0050661	0.50	NADP binding
GO:0034603	0.50	pyruvate dehydrogenase [NAD(P)+] activity
GO:0033218	0.50	amide 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	0.90	single-organism process
GO:0009987	0.89	cellular process
GO:0044763	0.86	single-organism cellular process
GO:0045454	0.80	cell redox homeostasis
GO:0008152	0.79	metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0044710	0.69	single-organism metabolic process
GO:0071704	0.66	organic substance metabolic process
GO:0044248	0.62	cellular catabolic process
GO:0055114	0.61	oxidation-reduction process
GO:1901575	0.60	organic substance catabolic process
GO:0006807	0.60	nitrogen compound metabolic process
GO:0044238	0.58	primary metabolic process
GO:1901360	0.56	organic cyclic compound metabolic process
GO:0046483	0.56	heterocycle metabolic process
GO:0043436	0.56	oxoacid metabolic process
GO:0043170	0.56	macromolecule metabolic process
GO:0034641	0.56	cellular nitrogen compound metabolic process
GO:0006725	0.56	cellular aromatic compound metabolic process
GO:1901564	0.54	organonitrogen compound metabolic process
GO:0044712	0.54	single-organism catabolic process
GO:0019752	0.54	carboxylic acid metabolic process
GO:0006139	0.54	nucleobase-containing compound metabolic process
GO:1901565	0.52	organonitrogen compound catabolic process
GO:0046395	0.52	carboxylic acid catabolic process
GO:0032787	0.52	monocarboxylic acid metabolic process
GO:0019538	0.52	protein metabolic process
GO:0006790	0.51	sulfur compound metabolic process
GO:0006520	0.51	cellular amino acid metabolic process
GO:0050812	0.50	regulation of acyl-CoA biosynthetic process
GO:0048598	0.50	embryonic morphogenesis
GO:0048469	0.50	cell maturation
GO:0046496	0.50	nicotinamide nucleotide metabolic process
GO:0044711	0.50	single-organism biosynthetic process
GO:0043648	0.50	dicarboxylic acid metabolic process
GO:0043603	0.50	cellular amide metabolic process
GO:0042775	0.50	mitochondrial ATP synthesis coupled electron transport
GO:0009081	0.50	branched-chain amino acid metabolic process
GO:0009068	0.50	aspartate family amino acid catabolic process
GO:0009063	0.50	cellular amino acid catabolic process
GO:0009060	0.50	aerobic respiration
GO:0007286	0.50	spermatid development
GO:0006553	0.50	lysine metabolic process
GO:0006090	0.50	pyruvate metabolic process
GO:0006085	0.50	acetyl-CoA biosynthetic 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	0.85	cell part
GO:0044424	0.79	intracellular part
GO:0044444	0.76	cytoplasmic part
GO:0005623	0.63	cell
GO:0043231	0.61	intracellular membrane-bounded organelle
GO:0005739	0.55	mitochondrion

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	1zmcD	0.811	1.95	0.125	0.930	1.8.1.4	NA
2	0.060	3ictA	0.790	1.88	0.203	0.915	1.8.1.14	1,37,48
3	0.060	1dxlA	0.798	1.88	0.168	0.922	1.8.1.4	NA
4	0.060	1dxlC	0.789	2.04	0.167	0.930	1.8.1.4	NA
5	0.060	2yquA	0.802	1.86	0.210	0.922	1.8.1.4	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.60	2gr0A	0.844	1.69	0.215	0.938	1.12	ADP	complex1.pdb.gz	4,6,38,39,40,41,43,59,60,61,62,66,67,125,126,127

	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.