D-I-TASSER Q99490-D2

D-I-TASSER results for Q99490-D2

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

Input Sequence in FASTA format

>Q99490 (117 residues)
SKTLDNSDLHPGPPAGSPPPLTLPPTPSPATAVTAASAQPPGPAPPITLEPPAPGLKRGR
ETKSTGGPPGSGPLPGPPSLSSGSGSRELLGAELRASPKAVINSQEWTLSRSIPELR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| SKTLDNSDLHPGPPAGSPPPLTLPPTPSPATAVTAASAQPPGPAPPITLEPPAPGLKRGRETKSTGGPPGSGPLPGPPSLSSGSGSRELLGAELRASPKAVINSQEWTLSRSIPELR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCSSCCCSSSSSCCCCCCC
Confidence	975666678889988999987778888852000002579999999844589997554564134468999999999996656787732232233303962112233034413564559
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| SKTLDNSDLHPGPPAGSPPPLTLPPTPSPATAVTAASAQPPGPAPPITLEPPAPGLKRGRETKSTGGPPGSGPLPGPPSLSSGSGSRELLGAELRASPKAVINSQEWTLSRSIPELR
Prediction	854366752443465444442424434444431433445444453414263445215434635446445474445334315645444411334145334331545514145415738
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCSSCCCSSSSSCCCCCCC
SKTLDNSDLHPGPPAGSPPPLTLPPTPSPATAVTAASAQPPGPAPPITLEPPAPGLKRGRETKSTGGPPGSGPLPGPPSLSSGSGSRELLGAELRASPKAVINSQEWTLSRSIPELR

7jtkA3

0.13

4.46

0.67

CEthreader

RSSFPNGDTYFGSYADDVKHGPGLYAFATGAGYAGEYAGGKRHGRGVMVFPDGGTYVGEVADKFEGQGQYRYPDGSVYTGSWAAGQKHGPGVYWDTARGCLRGELVGKGTYEQPALR

4r29A

0.06

2.57

0.43

EigenThreader

PEIKHDYFNESPNIYDITRVAEEFVNEKARRFSYMKTMYPEGSWLTVISGKRPEQRANRFIELYNIKRDIMQELPELKAVKSEMIIAREMGEIFSYMPGEIDSYMKYINNKL-----

3bboF

0.10

3.77

0.32

FFAS-3D

DRKLTKPEMGHLEKSGIIPLRQSIDGFEVTQKLDFGELFKEGDLSGTTIGKGFQGGIKRHNFKRGQMTHGSKSHRQLGSIGAGTTPGRVMPGRMGGTKRKIRKLKIVMIKGALPGKP

5jcss

0.11

3.97

1.18

SPARKS-K

NSDIDSMDILGGVDLTRQISYITEELTNIVREIISMNMKLSPNATAIMEGLNLLKYLLNNIVTPEKFQDFFSHLEGHPLLKTMSMNIEKMTEIITKEASV---KFEWFDGMLVKAVE

2ipzA

0.07

0.02

0.71

0.35

CNFpred

----------------------------------LVDKVEELLSKNYHLVNEVARLVKLVGER------------------------------------------------------

7lo5A

0.05

0.04

2.03

0.83

DEthreader

KGNNVRPDGYWEIFVLMQNFFEIADHHTLEFNIV-LVDLDYKEIDKYVSFDRPDAKHQVDEENDWNEFAIFKFNREIFHYVLYREKYALN------------LRQEFP--YKTVRGE

7jtkA3

0.10

0.09

3.52

0.95

MapAlign

-AFATGAGYAGEYAGGKRHGRGVMVFPDGGTYVGEFVADKFEGQGQYRYPDGSVYTGSWAAGQKHGPGVYWDTARGCLRGEWKKGLLVGKGTYEPALRFEGEFVRGMPAGTATYTL-

1r5sA

0.16

0.15

5.12

0.78

MUSTER

SPSKDCGSPKYAYFNGCSSPTAPLSPMSPPGYKLVTGDRNNSSCRNYNYSAEQNRMGQAGSTISSHAQPFDFPDDNQNAKKVAAGHELQPLAIVDQRPSSRASSR----SRPRPDLE

2wg6L

0.17

0.10

3.38

0.53

HHsearch

--------------------------------MKQLEDK------VEELLSKNYHLENEVALRS--APL-LVGSTGPKFVVNTSQY--INEEELKPGARVALNQQTLAIVNVLP---

3zq3A

0.01

1.13

0.52

CEthreader

---------EEASFERGNLDVDKLNGDWFSIVVASDKREKIEENGSMRVFVQHIDVLENSLG---FTFRIKENGVCTEFSLVADKTAKDGEYFVEYDGENTFTILKMFHLVNVNNGE

(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	0.5133

(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	5oy5A	0.44	4.09	0.011	0.718	model1_5oy5A.pdb.gz
2	6baoA2	0.44	4.19	0.032	0.735	model1_6baoA2.pdb.gz
3	5llwB3	0.44	4.26	0.108	0.744	model1_5llwB3.pdb.gz
4	5akpA	0.43	4.63	0.094	0.786	model1_5akpA.pdb.gz
5	1kdgB	0.43	4.64	0.028	0.786	model1_1kdgB.pdb.gz
6	1a0eA	0.43	4.78	0.019	0.786	model1_1a0eA.pdb.gz
7	6ptqA	0.43	4.75	0.076	0.786	model1_6ptqA.pdb.gz
8	4dmzA1	0.43	4.82	0.057	0.778	model1_4dmzA1.pdb.gz
9	4wkkA2	0.43	4.21	0.065	0.718	model1_4wkkA2.pdb.gz
10	3c2wC3	0.42	4.10	0.032	0.709	model1_3c2wC3.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:0019899	0.66	enzyme binding
GO:0030234	0.65	enzyme regulator activity
GO:0019901	0.65	protein kinase binding
GO:0030295	0.64	protein kinase activator activity
GO:1901363	0.54	heterocyclic compound binding
GO:0097159	0.54	organic cyclic compound binding
GO:0097367	0.50	carbohydrate derivative binding
GO:0000166	0.50	nucleotide 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:0043524	1.00	negative regulation of neuron apoptotic process
GO:0009987	0.73	cellular process
GO:0044699	0.72	single-organism process
GO:0080090	0.70	regulation of primary metabolic process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0051246	0.69	regulation of protein metabolic process
GO:0044763	0.69	single-organism cellular process
GO:0042177	0.68	negative regulation of protein catabolic process
GO:0048518	0.67	positive regulation of biological process
GO:0048522	0.66	positive regulation of cellular process
GO:0048584	0.65	positive regulation of response to stimulus
GO:0009966	0.65	regulation of signal transduction
GO:1902533	0.64	positive regulation of intracellular signal transduction

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:0044444	1.00	cytoplasmic part
GO:0005634	1.00	nucleus
GO:0044446	0.82	intracellular organelle part
GO:0044428	0.79	nuclear part
GO:0005739	0.78	mitochondrion
GO:0005730	0.78	nucleolus
GO:0016020	0.63	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	2ze9A	0.415	5.02	0.038	0.829	3.1.4.4	NA
2	0.060	1cf3A	0.430	4.61	0.038	0.752	1.1.3.4	NA
3	0.060	3fimB	0.431	4.49	0.019	0.744	1.1.3.7	NA
4	0.060	2f7fA	0.404	4.90	0.076	0.744	2.4.2.11	NA
5	0.060	1f5mB	0.417	4.73	0.101	0.752	1.8.4.14	23

	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	2jaxA	0.397	4.70	0.075	0.735	0.14	UUU	complex1.pdb.gz	19,20,91,92
2	0.01	2i5xA	0.414	4.68	0.057	0.769	0.17	UA5	complex2.pdb.gz	8,17,18,19
3	0.01	3cisB	0.420	4.92	0.060	0.803	0.23	ATP	complex3.pdb.gz	35,36,51,56,57
4	0.01	3cisA	0.426	4.50	0.052	0.761	0.13	ATP	complex4.pdb.gz	88,91,92,93,94
5	0.01	3c2wG	0.433	4.33	0.052	0.735	0.12	BLA	complex5.pdb.gz	28,50,53,56,93,95
6	0.01	3jpuE	0.425	4.35	0.071	0.727	0.18	TY4	complex6.pdb.gz	9,10,21,36,39,77
7	0.01	3ix8D	0.420	4.35	0.079	0.718	0.14	TX3	complex7.pdb.gz	4,9,11,75
8	0.01	2o9bA	0.388	4.52	0.089	0.701	0.15	LBV	complex8.pdb.gz	26,35,81,83,87
9	0.01	3k30B	0.420	4.48	0.087	0.727	0.13	ADP	complex9.pdb.gz	12,13,19,20
10	0.01	2o9c0	0.421	4.61	0.088	0.761	0.10	III	complex10.pdb.gz	72,74,100

	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.