D-I-TASSER O15146-D4

D-I-TASSER results for O15146-D4

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

Input Sequence in FASTA format

>O15146 (161 residues)
EWSKPQKDNKGYCAQYRGEVCNAVLAKDALVFLNTSYADPEEAQELLVHTAWNELKVVSP
VCRPAAEALLCNHIFQECSPGVVPTPIPICREYCLAVKELFCAKEWLVMEEKTHRGLYRS
EMHLLSVPECSKLPSMHWDPTACARLPHLDYNKENLKTFPP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| EWSKPQKDNKGYCAQYRGEVCNAVLAKDALVFLNTSYADPEEAQELLVHTAWNELKVVSPVCRPAAEALLCNHIFQECSPGVVPTPIPICREYCLAVKELFCAKEWLVMEEKTHRGLYRSEMHLLSVPECSKLPSMHWDPTACARLPHLDYNKENLKTFPP
Prediction	CCCCCCCCCCCSCSCCCCHHHHHHCCCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCC
Confidence	95324578897412035377798618982999718988889999999999999854416789999999999981888889999877645499999999820779999999722227642234654698833278889998864355875334002677899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| EWSKPQKDNKGYCAQYRGEVCNAVLAKDALVFLNTSYADPEEAQELLVHTAWNELKVVSPVCRPAAEALLCNHIFQECSPGVVPTPIPICREYCLAVKELFCAKEWLVMEEKTHRGLYRSEMHLLSVPECSKLPSMHWDPTACARLPHLDYNKENLKTFPP
Prediction	82565377671314514251045206652000003437434421441043015305503740462034100220123047664442350046204303742146104304634745334543431413405602546654531230323425575356468
	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                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCSCSCCCCHHHHHHCCCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCC
EWSKPQKDNKGYCAQYRGEVCNAVLAKDALVFLNTSYADPEEAQELLVHTAWNELKVVSPVCRPAAEALLCNHIFQECSPGVVPTPIPICREYCLAVKELFCAKEWLVMEEKTHRGLYRSEMHLLSVPECSKLPSMHWDPTACARLPHLDYNKENLKTFPP

3hklB

0.71

0.61

17.29

1.17

DEthreader

---GSKG----YCAQYRGEVCDAVLVDSLVFFNTSY-PDPEEAQELLIHTAWNELKAVSPLCRPAAEALLCNHLFQECSPGVLPTPMPICREYCLAVKELFCAKEWME-KTRGLYR------HFLPVPECSKLPSMHQDPTACTRLPYL----TFPS----

3hklB

0.80

0.76

21.58

3.04

SPARKS-K

----GPRGSKGYCAQYRGEVCDAVLVKDSLVFFNTSYPDPEEAQELLIHTAWNELKAVSPLCRPAAEALLCNHLFQECSPGVLPTPMPICREYCLAVKELFCAKEWLAMEGKTHRGLYRSGMHFLPVPECSKLPSMHQDPTACTRLPYLDYKTFPSI----

3hklB

0.81

0.72

20.35

1.58

MapAlign

------RGSKGYCAQYRGEVCDAVLVDSLVFFNTS-YPDPEEAQELLIHTAWNELKAVSPLCRPAAEALLCNHLFQECSPGVLPTPMPICREYCLAVKELFCAKEWLAMEGKTHRGLYRSGMHFLPVPECSKLPSMHQDPTACTRLPYLDY----------

3hklB

0.80

0.76

21.58

1.56

CEthreader

----GPRGSKGYCAQYRGEVCDAVLVKDSLVFFNTSYPDPEEAQELLIHTAWNELKAVSPLCRPAAEALLCNHLFQECSPGVLPTPMPICREYCLAVKELFCAKEWLAMEGKTHRGLYRSGMHFLPVPECSKLPSMHQDPTACTRLPYLDYKTFPSI----

3hklB

0.80

0.76

21.58

2.80

MUSTER

----GPRGSKGYCAQYRGEVCDAVLVKDSLVFFNTSYPDPEEAQELLIHTAWNELKAVSPLCRPAAEALLCNHLFQECSPGVLPTPMPICREYCLAVKELFCAKEWLAMEGKTHRGLYRSGMHFLPVPECSKLPSMHQDPTACTRLPYLDYKTFPSI----

3hklB

0.80

0.76

21.58

5.81

HHsearch

----GPRGSKGYCAQYRGEVCDAVLVKDSLVFFNTSYPDPEEAQELLIHTAWNELKAVSPLCRPAAEALLCNHLFQECSPGVLPTPMPICREYCLAVKELFCAKEWLAMEGKTHRGLYRSGMHFLPVPECSKLPSMHQDPTACTRLPYLDYKTFPSI----

3hklB

0.83

0.78

22.07

1.99

FFAS-3D

----GPRGSKGYCAQYRGEVCDAVLVKDSLVFFNTSYPDPEEAQELLIHTAWNELKAVSPLCRPAAEALLCNHLFQECSPGVLPTPMPICREYCLAVKELFCAKEWLAMEGKTHRGLYRSGMHFLPVPECSKLPSMHQDPTACTRLPYLDYK-----TFPS

3hklB

0.77

0.73

20.57

1.62

EigenThreader

----GPRGSKGYCAQYRGEVCDAVLVKSLVFFNTS-YPDPEEAQELLIHTAWNELKAVSPLCRPAAEALLCNHLFQECSPGVLPTPMPICREYCLAVKELFCAKEWLAMEGKTHRGLYRSGMHFLPVPECSKLPSMHQDPTACTRLPYLDYKT----FPSI

3hklA

0.87

0.76

21.34

2.41

CNFpred

---------KGYCAQYRGEVCDAVLVKDSLVFFNTSYPDPEEAQELLIHTAWNELKAVSPLCRPAAEALLCNHLFQECSPGVLPTPMPICREYCLAVKELFCAKEWLAMEGKTHRGLYRSGMHFLPVPECSKLPSMHQDPTACTRLPYLD-----------

6r4lA

0.08

0.07

2.70

1.00

DEthreader

APVPRSF-E--PPVLTSLVVCGEEWKVRYACC-------TKDQVVALRDNLQKAQPLISCPCLKNFNNLFCHFTCAAD-----QGRFFMNSSWASEFYDSCKNYAMDLIGGFLGDA--KPMLGG-S-PF-QINYK--EEWQEFNDEVYACDDQESCHQH-P

(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	0.7594

(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	3hklB	0.88	1.66	0.770	0.944	model1_3hklB.pdb.gz
2	1ijyA	0.57	3.25	0.217	0.745	model1_1ijyA.pdb.gz
3	3qntA	0.57	4.06	0.063	0.839	model1_3qntA.pdb.gz
4	3jd8A	0.57	4.03	0.084	0.820	model1_3jd8A.pdb.gz
5	3gkhA	0.56	4.09	0.080	0.832	model1_3gkhA.pdb.gz
6	5t44A	0.56	2.98	0.198	0.714	model1_5t44A.pdb.gz
7	5l7dA	0.56	3.78	0.145	0.776	model1_5l7dA.pdb.gz
8	1ijxA	0.56	3.45	0.161	0.745	model1_1ijxA.pdb.gz
9	6v3fA	0.56	4.18	0.074	0.839	model1_6v3fA.pdb.gz
10	5bpbA	0.56	3.07	0.231	0.721	model1_5bpbA.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:0003824	0.56	catalytic activity
GO:0042802	0.54	identical protein binding
GO:0016740	0.50	transferase activity

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:0050794	0.98	regulation of cellular process
GO:0009987	0.96	cellular process
GO:0051960	0.94	regulation of nervous system development
GO:0051128	0.94	regulation of cellular component organization
GO:0048638	0.94	regulation of developmental growth
GO:0044699	0.94	single-organism process
GO:0044763	0.93	single-organism cellular process
GO:0016043	0.90	cellular component organization
GO:0050808	0.86	synapse organization
GO:0043113	0.86	receptor clustering
GO:0007528	0.85	neuromuscular junction development
GO:0071340	0.74	skeletal muscle acetylcholine-gated channel clustering
GO:0032502	0.64	developmental process
GO:0048519	0.63	negative regulation of biological process
GO:0044767	0.63	single-organism developmental process
GO:0008152	0.60	metabolic process
GO:0071704	0.57	organic substance metabolic process
GO:0006928	0.57	movement of cell or subcellular component
GO:0044238	0.56	primary metabolic process
GO:0044237	0.56	cellular metabolic process
GO:0007411	0.56	axon guidance
GO:0043170	0.54	macromolecule metabolic process
GO:0044260	0.53	cellular macromolecule metabolic process
GO:0048523	0.52	negative regulation of cellular process
GO:0022607	0.51	cellular component assembly
GO:0051124	0.50	synaptic growth at neuromuscular junction
GO:0030517	0.50	negative regulation of axon extension
GO:0008045	0.50	motor neuron axon guidance

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:0016020	0.98	membrane
GO:0044425	0.89	membrane part
GO:0044459	0.88	plasma membrane part
GO:0098590	0.73	plasma membrane region
GO:0044456	0.73	synapse part
GO:0044424	0.73	intracellular part
GO:0045211	0.72	postsynaptic 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	0.532	3hklB	0.881	1.66	0.770	0.944	2.7.10.1	25,32,73,76,78,88,92,128,133,143,145,147
2	0.060	1jqoA	0.431	5.20	0.053	0.733	4.1.1.31	NA
3	0.060	1vljB	0.427	5.22	0.084	0.758	1.1.1.-	NA
4	0.060	1yiqA	0.423	4.96	0.047	0.714	1.1.99.-	NA
5	0.060	2qykB	0.436	5.60	0.061	0.807	3.1.4.17	73

	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	3sl6C	0.426	5.64	0.075	0.795	0.18	JN8	complex1.pdb.gz	12,18,21
2	0.01	3g4gB	0.424	5.61	0.076	0.789	0.11	D71	complex2.pdb.gz	71,72,75
3	0.01	3sl4A	0.427	5.62	0.071	0.801	0.11	JN4	complex3.pdb.gz	12,14,15
4	0.01	1xm6A	0.424	5.36	0.033	0.776	0.15	5RM	complex4.pdb.gz	17,18,28,29
5	0.01	1pyyA	0.434	5.54	0.054	0.807	0.21	OSU	complex5.pdb.gz	11,12,13,14,16,17,18
6	0.01	3g4gC	0.421	5.60	0.092	0.789	0.11	D71	complex6.pdb.gz	48,75,76
7	0.01	3sl5A	0.432	5.48	0.076	0.795	0.12	J25	complex7.pdb.gz	12,17,22
8	0.01	2fm0D	0.437	5.55	0.084	0.807	0.14	M98	complex8.pdb.gz	90,93,94,97
9	0.01	1qmfA	0.348	5.82	0.042	0.671	0.15	CES	complex9.pdb.gz	11,12,13,14

	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.