D-I-TASSER O00238-D2

D-I-TASSER results for O00238-D2

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

Input Sequence in FASTA format

>O00238 (123 residues)
IGLEQDETYIPPGESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWM
GKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITD
YHE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| IGLEQDETYIPPGESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDYHE
Prediction	CCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCHHHCSSSSSSSSCCCSSSSSSSSCCSSSSSSSSCCCCHHHHHHHHHHHHHHCCCCCCSCSSSSSSSCCCCCCCSSSSSSSSCC
Confidence	975789731488652788876136889998985421234655636667886247618999999994879999567555589999999997338993122378899717999854799984159
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| IGLEQDETYIPPGESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDYHE
Prediction	771757733246563145225544644444334313643326405015301533203012042464400003045754534423410440551514100200000234674443000001428
	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 DeepPotential. 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

CCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCHHHCSSSSSSSSCCCSSSSSSSSCCSSSSSSSSCCCCHHHHHHHHHHHHHHCCCCCCSCSSSSSSSCCCCCCCSSSSSSSSCC
IGLEQDETYIPPGESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDYHE

6tpaA

0.18

0.14

4.49

1.00

DEthreader

MDFKVKLSSE------------------------RE-R-VEDLFEYEGCKVGRTYGHVYKAKRDDKDYALKQIEGTGISSACREIALLRE-L-KHPNVISLQKVFLSHA--DRKVWLLFDYAM

3mdyA1

1.00

0.88

24.59

2.10

SPARKS-K

-------------ESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDY--

3mdyA

1.00

0.89

25.04

0.50

MapAlign

-------------ESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDYHE

3mdyA

1.00

0.89

25.04

0.31

CEthreader

-------------ESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDYHE

3mdyA

1.00

0.89

25.04

1.52

MUSTER

-------------ESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDYHE

3h9rA1

0.61

0.55

15.83

0.65

HHsearch

-------TTNVGDSTLADLLDHSCTSGSGSGLPFLVQRTVARQITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTS---STQLWLITHY--

3mdyA1

1.00

0.88

24.59

2.07

FFAS-3D

-------------ESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDY--

1qcfA

0.22

0.20

6.41

0.60

EigenThreader

GGFYISPRSTF--STLQELVDHYKKGNDGLCQKLDAWEIPRESLKLEKKLGAGQFGEVWMATYNKTKVAVKTMKPGSMEAFLAEANVMKT--LQHDKLVKLHAVVT-----KEPIYIITEFMA

3mdyA

1.00

0.89

25.04

1.71

CNFpred

-------------ESLRDLIEQSQSSGSGSGLPLLVQRTIAKQIQMVKQIGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQTVLMRHENILGFIAADIKGTGSWTQLYLITDYHE

2vd5A1

0.20

0.15

4.93

1.00

DEthreader

LFWAEIVV-R----------------------LKEVR-LQRDDFEILKVIGRGAFSEVAVVKMKGQVYAMKIMNKDMLSCFREERDVLVNGD-RR-WITQLHFAFQDE----NYLYLVMEYYV

(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	0.7424

(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 DeepPotential, 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	3kcfC	0.85	1.24	0.655	0.919	model1_3kcfC.pdb.gz
2	3mdyA	0.84	1.23	1.000	0.894	model1_3mdyA.pdb.gz
3	3h9rA	0.81	1.82	0.589	0.894	model1_3h9rA.pdb.gz
4	1k9aB	0.69	3.19	0.232	0.886	model1_1k9aB.pdb.gz
5	3g2fA1	0.64	1.82	0.326	0.699	model1_3g2fA1.pdb.gz
6	2qluA	0.63	1.04	0.390	0.667	model1_2qluA.pdb.gz
7	4y93A	0.63	2.97	0.208	0.813	model1_4y93A.pdb.gz
8	5e8vA	0.63	1.71	0.393	0.683	model1_5e8vA.pdb.gz
9	2acxA	0.62	2.99	0.148	0.772	model1_2acxA.pdb.gz
10	2fo0A	0.62	3.27	0.196	0.797	model1_2fo0A.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:0016740	0.93	transferase activity
GO:0004672	0.92	protein kinase activity
GO:0004871	0.69	signal transducer activity
GO:0004674	0.69	protein serine/threonine kinase activity
GO:0004872	0.66	receptor activity
GO:0019199	0.65	transmembrane receptor protein kinase activity
GO:0004675	0.64	transmembrane receptor protein serine/threonine kinase activity
GO:0005024	0.54	transforming growth factor beta-activated receptor activity
GO:0005025	0.51	transforming growth factor beta receptor activity, type I
GO:0019838	0.50	growth factor 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:0065007	0.98	biological regulation
GO:0050789	0.97	regulation of biological process
GO:0044699	0.97	single-organism process
GO:0009987	0.96	cellular process
GO:0050794	0.93	regulation of cellular process
GO:0032502	0.91	developmental process
GO:0044767	0.87	single-organism developmental process
GO:0044763	0.86	single-organism cellular process
GO:0048518	0.84	positive regulation of biological process
GO:0048856	0.83	anatomical structure development
GO:0048869	0.82	cellular developmental process
GO:0051239	0.79	regulation of multicellular organismal process
GO:0009653	0.77	anatomical structure morphogenesis
GO:0050793	0.76	regulation of developmental process
GO:2000026	0.74	regulation of multicellular organismal development
GO:0008152	0.72	metabolic process
GO:0044260	0.71	cellular macromolecule metabolic process
GO:0042127	0.71	regulation of cell proliferation
GO:0048519	0.58	negative regulation of biological process
GO:0051240	0.55	positive regulation of multicellular organismal process
GO:0048523	0.55	negative regulation of cellular process
GO:0051094	0.54	positive regulation of developmental process
GO:0007165	0.54	signal transduction
GO:0009887	0.51	organ morphogenesis
GO:0007166	0.51	cell surface receptor signaling pathway
GO:0019222	0.50	regulation of metabolic process
GO:0007167	0.50	enzyme linked receptor protein signaling pathway

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:0016020	0.71	membrane
GO:0044424	0.63	intracellular part
GO:0044425	0.52	membrane 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	0.060	2ofuA	0.590	2.30	0.247	0.691	2.7.10.2	NA
2	0.060	2gqgA	0.596	2.60	0.226	0.715	2.7.10.2	NA
3	0.060	2fo0A	0.619	3.27	0.196	0.797	2.7.10.2	NA
4	0.060	2acxA	0.621	2.99	0.148	0.772	2.7.11.16	NA
5	0.060	1iasA	0.842	1.41	0.655	0.919	2.7.11.30 2.7.1.37	52

	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	0.92	3mdyA	0.836	1.23	1.000	0.894	0.92	LDN	complex1.pdb.gz	50,58,69,99,119,120,121,122,123
2	0.75	3faaB	0.868	1.19	0.693	0.927	1.04	55F	complex2.pdb.gz	50,58,69,71,84,88,99,117,118,119,121
3	0.39	3g2fA	0.643	1.82	0.326	0.699	0.95	ADP	complex3.pdb.gz	50,51,52,53,55,56,58,69,71,119,120,122
4	0.36	1b6c1	0.805	1.67	0.700	0.894	1.34	III	complex4.pdb.gz	33,34,35,37,38,39,81,82,85,86,89,90,104,106
5	0.04	2hz4C	0.553	1.81	0.234	0.626	1.14	4ST	complex5.pdb.gz	63,100,102

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.