D-I-TASSER Q5W5X9-D4

D-I-TASSER results for Q5W5X9-D4

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

Input Sequence in FASTA format

>Q5W5X9 (98 residues)
DFSPEVAETYRLLGGADLAQGNHSGARKKLKKCLQIQTLLYGPQDKRTLATQQAMGMLST
APKVASKPRQASKAKVAFCTSIPQDTLLGKARPGTTAD

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| DFSPEVAETYRLLGGADLAQGNHSGARKKLKKCLQIQTLLYGPQDKRTLATQQAMGMLSTAPKVASKPRQASKAKVAFCTSIPQDTLLGKARPGTTAD
Prediction	CCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCHHHHCCCCCCCHHHCHHHHHCCCCCCCCCCCCCCCCC
Confidence	98789999999998899983768999999999999999983899821599999999999721221122333100001342013445678888775689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| DFSPEVAETYRLLGGADLAQGNHSGARKKLKKCLQIQTLLYGPQDKRTLATQQAMGMLSTAPKVASKPRQASKAKVAFCTSIPQDTLLGKARPGTTAD
Prediction	84556104014311312134253550253044024013322157354354145115203524634455464665434034324544444444554568
	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

                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCHHHHCCCCCCCHHHCHHHHHCCCCCCCCCCCCCCCCC
DFSPEVAETYRLLGGADLAQGNHSGARKKLKKCLQIQTLLYGPQDKRTLATQQAMGMLSTAPKVASKPRQASKAKVAFCTSIPQDTLLGKARPGTTAD

2yinA

0.08

0.07

2.84

1.17

DEthreader

KWRQLKETLYETIIGYFDKGKMWEEAISLCKELAEQYEMEIFD-YELLSQNLIQQAKFYESIKI-LRPKPGKEYERRDFQ-MQLMTQF------LRWF

3n71A4

0.09

0.07

2.77

1.44

SPARKS-K

HNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREAALNN----------------

5o09C

0.14

0.13

4.55

1.05

MUSTER

EESDKVATIKNNLAMIFKQLRKFERAEGYYCEALETFQRLDGEQSARVASVYNNLGVLYYSHMDVDRAQVMHERALAIRQNL---HEGQMDPADLSQT

4y6cA2

0.16

0.14

4.78

1.44

FFAS-3D

HEHPSRLRSQHELARRYQQNGQVQEAVELLEQVVAIQAKTLRSEHPSRLASQHELARAYAN-GQVQEAVELLEQVVAIQ-----AKTLRSEHPSRL--

6tgbA

0.05

2.31

1.00

DEthreader

KWRQLKETLYETIIGYFDKGKMWEEAISLCKELAEQYEMEIFDY-ELLSQNLIQQAKFYESIILRP-KPDKEYERREDFQ-MQLMTQFP----CLRWF

6t3hA3

0.11

0.09

3.32

1.24

SPARKS-K

-EETKFAEFHYKIGVAYYEIDQHLVSVNKVTKARDIYKKSD-MWNLEAIQCSLVVGINLYDMGRLDDADAYFRDALTEALDHGY--------------

3n71A4

0.09

0.07

2.73

0.55

MapAlign

HNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREAA-------------------

3n71A

0.09

0.07

2.77

0.39

CEthreader

HNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREAALNN----------------

3qwvA2

0.16

0.15

5.07

1.04

MUSTER

DSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLE------NKAAGEKALKKAIAIEVAHGKDHPYISEI

5o09C

0.20

6.51

0.81

HHsearch

EQSARVASVYNNLGVLYYSHMDVDRAQVMHERALAIRQNLHEGDPADLSQTFINLGAVYKAAGDFQKAEAVDRAKRIRAAMNGDTAELRKQDPDLTGI

(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	0.7064

(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	6w2wA	0.70	3.03	0.086	0.929	model1_6w2wA.pdb.gz
2	6n1lA	0.68	2.68	0.058	0.867	model1_6n1lA.pdb.gz
3	5xsdL	0.68	2.86	0.053	0.888	model1_5xsdL.pdb.gz
4	6m31A2	0.67	2.55	0.106	0.867	model1_6m31A2.pdb.gz
5	1oczC2	0.67	2.77	0.043	0.857	model1_1oczC2.pdb.gz
6	2yevA2	0.67	2.75	0.108	0.857	model1_2yevA2.pdb.gz
7	2l10A	0.66	2.43	0.043	0.857	model1_2l10A.pdb.gz
8	4o6yA	0.66	3.08	0.041	0.929	model1_4o6yA.pdb.gz
9	7jroc	0.66	3.19	0.084	0.898	model1_7jroc.pdb.gz
10	3kyjA	0.66	2.89	0.076	0.918	model1_3kyjA.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:0097159	0.29	organic cyclic compound binding
GO:1901363	0.23	heterocyclic compound binding
GO:0043167	0.23	ion binding
GO:0046872	0.20	metal ion binding
GO:0003824	0.19	catalytic activity
GO:0005215	0.18	transporter activity
GO:0097367	0.17	carbohydrate derivative binding
GO:0046914	0.17	transition metal ion binding
GO:0036094	0.16	small molecule binding
GO:0022891	0.15	substrate-specific transmembrane transporter activity
GO:0003676	0.13	nucleic acid binding
GO:0015075	0.12	ion transmembrane transporter activity
GO:0035639	0.11	purine ribonucleoside triphosphate binding
GO:0032555	0.11	purine ribonucleotide binding
GO:0032550	0.11	purine ribonucleoside binding
GO:0008289	0.11	lipid binding
GO:0005506	0.11	iron ion binding
GO:0005102	0.11	receptor 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	0.78	single-organism process
GO:0009987	0.74	cellular process
GO:0044763	0.58	single-organism cellular process
GO:0051179	0.56	localization
GO:0071840	0.50	cellular component organization or biogenesis

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	0.98	cell part
GO:0044424	0.92	intracellular part
GO:0016020	0.76	membrane
GO:0043226	0.72	organelle
GO:0044422	0.67	organelle part
GO:0044446	0.64	intracellular organelle part
GO:0043229	0.58	intracellular organelle
GO:0043227	0.58	membrane-bounded organelle
GO:0044444	0.54	cytoplasmic part
GO:0005737	0.52	cytoplasm
GO:0044430	0.50	cytoskeletal part

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	0.081	3gm1B	0.629	2.97	0.122	0.888	2.7.10.2	74
2	0.067	3eziA	0.615	2.83	0.065	0.867	2.7.13.3	NA
3	0.066	2kk1A	0.601	3.30	0.101	0.898	2.7.10.2	12,50
4	0.066	1i5nD	0.643	3.06	0.066	0.888	2.7.13.3	48,78
5	0.060	1g4wR	0.497	4.19	0.111	0.898	3.1.3.48	17

	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	0.02	2ff4B	0.628	3.24	0.105	0.867	0.65	III	complex1.pdb.gz	14,21,22,23,26,27
2	0.02	2ff4A	0.630	3.16	0.105	0.867	0.45	III	complex2.pdb.gz	16,17,18,19,20,25,26
3	0.01	3abkP	0.671	2.74	0.043	0.857	0.46	CDL	complex3.pdb.gz	28,29,33,36,37,40,42
4	0.01	2fynJ	0.606	3.29	0.031	0.878	0.50	HEM	complex4.pdb.gz	14,15,18,19,26,30,54,58,59,61,62,74,75
5	0.01	3ag4C	0.564	3.34	0.043	0.898	0.55	CDL	complex5.pdb.gz	11,15,18
6	0.01	2eimC	0.566	3.34	0.043	0.898	0.40	CDL	complex6.pdb.gz	8,12,15,34

	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.