D-I-TASSER O15287-D2

D-I-TASSER results for O15287-D2

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

Input Sequence in FASTA format

>O15287 (97 residues)
VGLQAALWLSADRLGDLALLLETLNGSQSGASKDLLLLLKTWSPPAEELDAPLTLQDAQG
LKDVLLTAFAYRQGLQELITGNPDKALSSLHEAASGL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| VGLQAALWLSADRLGDLALLLETLNGSQSGASKDLLLLLKTWSPPAEELDAPLTLQDAQGLKDVLLTAFAYRQGLQELITGNPDKALSSLHEAASGL
Prediction	CCHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCSSSCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC
Confidence	9216889986324658999999953110234547999998449996557887132357899999999999999999998368178999999997139
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| VGLQAALWLSADRLGDLALLLETLNGSQSGASKDLLLLLKTWSPPAEELDAPLTLQDAQGLKDVLLTAFAYRQGLQELITGNPDKALSSLHEAASGL
Prediction	8524111112363154023004303454553554013104325245755623131451750341012222134114414465245124304533768
	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

                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCSSSCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC
VGLQAALWLSADRLGDLALLLETLNGSQSGASKDLLLLLKTWSPPAEELDAPLTLQDAQGLKDVLLTAFAYRQGLQELITGNPDKALSSLHEAASGL

4cuoA

0.07

0.06

2.54

1.00

DEthreader

QLT--PTYR-PNVTSIVRGVIQDALQTDRIRGFDVVDNIKTAVNAC-----PG-VVSCADILTIAAEQSV-WGPSFD---NQSAFFNSFVASMIKGN

2gw1A4

0.13

0.12

4.31

0.46

CEthreader

ELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKA---ARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELF

6w08A

0.06

2.64

0.48

EigenThreader

QLQTDIPASISAMVLLNSACQGVVETNLNAVQKLVRQWRLSGNLYF---SNDIMDSVLSIANTFKDSNVQILTLFKALETRFDTAQLQQLTSLILTL

6t3hA1

0.13

0.12

4.31

0.63

FFAS-3D

---KWHDYIMQEKVHESIEKRTEIKQLLSQAEDNLDHRHSLCFDQEASMGDVVNMLSKGSHDLLINFYFELFAGDYEFFKKNYVKAISFYEKAEQKL

6w2wA2

0.14

0.13

4.55

0.71

SPARKS-K

NEAAKECLKAVRAALEAALLALLLLAKHPGSAQDAVQLATAAQLAKQYPNS-------DIAKKCIKAASEAAEEASKAAEEDSQKARDEIKEASQKA

3um3A

0.16

0.12

4.12

0.53

CNFpred

--PGLIAALAYETANFYQKADHTLSSLEPAYSAKWRKYLHL-------------------KMCFYTAYAYCYHGETLLASDKCGEAIRSLQEAEKLY

4atjA

0.04

0.03

1.70

1.00

DEthreader

QLT--PTYD-PNVSNIVRDTIVNELRSDPRIGFPVIDRMKAAVEACP---RT--VSC-ADLLTIAAQQSV-TGPSFD---STQTFFNAFVEAMDRMG

1ouvA

0.09

3.48

0.63

MapAlign

--KYFEKACDLKESGCFNLGVLYYGQGVEKNLKKAASFYAKANLYYSGQGVSQNTNKALQYYSKACAEGCASLGGIYHDTRDFKKAVEYFTKACDLN

3racA2

0.18

5.69

0.55

MUSTER

ARLVPRLLDALGISASLSRAFLAC-QLHAAKDVDLLANLLTWSPAERDAAKRSREASDRELEALLRDAPRAAADVRDAWR---YLCRLAEALHDSGL

2hr2A1

0.23

0.09

2.91

0.51

HHsearch

----------------------------------------------------------KPLKEVVGAYLALSDAQRQLVAGEYDEAAANCRRAEISH

(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	0.819

(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	6z16A2	0.61	3.18	0.137	0.897	model1_6z16A2.pdb.gz
2	4akkA	0.60	3.58	0.108	0.949	model1_4akkA.pdb.gz
3	6m5aA2	0.60	3.54	0.086	0.866	model1_6m5aA2.pdb.gz
4	6krjA	0.59	3.81	0.095	0.949	model1_6krjA.pdb.gz
5	2i3fA	0.59	3.64	0.045	0.917	model1_2i3fA.pdb.gz
6	6i60A2	0.59	3.64	0.103	0.845	model1_6i60A2.pdb.gz
7	8e9gL	0.59	3.14	0.085	0.866	model1_8e9gL.pdb.gz
8	3c68A2	0.59	3.63	0.073	0.866	model1_3c68A2.pdb.gz
9	4nt1A	0.54	3.39	0.048	0.845	model1_4nt1A.pdb.gz
10	2evsA	0.47	3.76	0.112	0.783	model1_2evsA.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:0003684	1.00	damaged DNA 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:0006974	1.00	cellular response to DNA damage stimulus
GO:0016043	0.82	cellular component organization
GO:0006996	0.81	organelle organization
GO:0008152	0.80	metabolic process
GO:0007005	0.80	mitochondrion organization
GO:0071704	0.79	organic substance metabolic process
GO:0044260	0.78	cellular macromolecule metabolic process
GO:0044238	0.78	primary metabolic process
GO:0034641	0.76	cellular nitrogen compound metabolic process
GO:0090304	0.75	nucleic acid metabolic process
GO:0006259	0.74	DNA metabolic process
GO:0006281	0.70	DNA repair
GO:0022402	0.51	cell cycle 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:0044428	1.00	nuclear part
GO:0043226	0.91	organelle
GO:0043229	0.90	intracellular organelle
GO:0043232	0.88	intracellular non-membrane-bounded organelle
GO:0016020	0.88	membrane
GO:0005886	0.87	plasma membrane
GO:0005737	0.87	cytoplasm
GO:0005730	0.87	nucleolus
GO:0032991	0.67	macromolecular complex
GO:0043234	0.66	protein complex
GO:0043227	0.65	membrane-bounded organelle
GO:0043231	0.64	intracellular membrane-bounded organelle
GO:0044444	0.63	cytoplasmic part
GO:0044451	0.59	nucleoplasm part
GO:0043240	0.57	Fanconi anaemia nuclear complex
GO:0005739	0.55	mitochondrion
GO:0005654	0.50	nucleoplasm

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	1ug9A	0.563	3.63	0.092	0.814	3.2.1.70	NA
2	0.060	3lxuX	0.530	3.65	0.100	0.825	3.4.14.10	NA
3	0.060	2ixnA	0.550	3.31	0.059	0.856	5.2.1.8	NA
4	0.060	2htnG	0.528	2.59	0.042	0.649	1.16.3.1	NA
5	0.060	1dliA	0.516	3.74	0.108	0.804	1.1.1.22	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:

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	3c3qA	0.572	3.31	0.099	0.814	0.32	III	complex1.pdb.gz	12,14,15,18,19,78
2	0.01	2xs8A	0.561	3.42	0.090	0.804	0.24	III	complex2.pdb.gz	14,68,71,72
3	0.01	3goiA	0.583	3.62	0.087	0.917	0.18	LOI	complex3.pdb.gz	17,18,21
4	0.01	3h1vX	0.585	3.61	0.087	0.917	0.16	TK1	complex4.pdb.gz	75,76,79,80
5	0.01	3c67A	0.587	3.66	0.073	0.866	0.21	GLC	complex5.pdb.gz	16,17,18,19
6	0.01	1lf9A	0.562	3.69	0.092	0.825	0.10	ACR	complex6.pdb.gz	18,37,38
7	0.01	2pywA	0.554	3.94	0.074	0.938	0.21	ADP	complex7.pdb.gz	15,16,17,18,36,74
8	0.01	2fzf0	0.551	2.97	0.067	0.753	0.21	III	complex8.pdb.gz	14,57,60,61,63,65,68,69,71,72,75,78,79
9	0.01	3fguA	0.457	4.57	0.047	0.835	0.12	ANP	complex9.pdb.gz	32,34,35,73,74,77

	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.