D-I-TASSER O15287-D3

D-I-TASSER results for O15287-D3

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

Input Sequence in FASTA format

>O15287 (76 residues)
CPRPVLVQVYTALGSCHRKMGNPQRALLYLVAALKEGSAWGPPLLEASRLYQQLGDTTAE
LESLELLVEALNVPCS

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| CPRPVLVQVYTALGSCHRKMGNPQRALLYLVAALKEGSAWGPPLLEASRLYQQLGDTTAELESLELLVEALNVPCS
Prediction	CCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Confidence	9815999999999999999399089999999999638631089999999999968929999999999999814689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| CPRPVLVQVYTALGSCHRKMGNPQRALLYLVAALKEGSAWGPPLLEASRLYQQLGDTTAELESLELLVEALNVPCS
Prediction	8644011202312130254274243003203411545242233124113114526536341510421152254548
	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

                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
CPRPVLVQVYTALGSCHRKMGNPQRALLYLVAALKEGSAWGPPLLEASRLYQQLGDTTAELESLELLVEALNVPCS

5o09C

0.18

0.17

5.58

1.50

DEthreader

QDPDLLTGIYSLLAHLYDRWGRMDKAAEFYELALKISEEVATIKNNLAMIFKQLR-K--FERAEGYYCEALETFQR

4gcoA1

0.15

0.14

4.87

1.44

SPARKS-K

YINPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEF---QRALDDCDTCIRLDSK

6vl6A1

0.14

0.13

4.49

1.40

FFAS-3D

-SMGNLAEKMYKAGNAMYRKGQYTIAIIAYTLALLKDPNNAEAWYNLGNAAYKKGEYDEAIEAYQ---KALELDP-

4gyoA

0.13

4.55

1.50

DEthreader

EEAYMIAAAYYNVGHCKYSLGDYKEAEGYFKTAAAIFEFAVQAVFSLTHIYCKEGKYDKAVEAYDRGIKSAAEWED

5lynA1

0.10

0.09

3.45

1.40

SPARKS-K

AETKAKAEDLKMQGNKAMANKDYELAINKYTEAIKVLPTNAIYYANRAAAHSSLKEY---DQAVKDAESAISIDPS

1zu2A

0.12

4.16

0.47

MapAlign

-SNPLDADNLTRWGGVLLELSMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAAKHNFDLATQFFQQAVDEQ--

6i57A

0.16

5.22

0.31

CEthreader

KINNKECAIYTNRALCYLKLCQFEEAKQDCDQALQLADGNVKAFYRRALAHKGLKN---YQKSLIDLNKVILLDPS

2xcbA

0.14

4.91

0.96

MUSTER

MLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECHLQLGDLDGAESGFYSARALAAAQPA

3pe3A

0.18

0.17

5.58

0.52

HHsearch

RISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIAS---YRTALKLKPD

2q7fA1

0.17

0.16

5.20

1.40

FFAS-3D

--NKEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFE---KALRAGME

(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	0.871

(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	4gcnA1	0.89	1.56	0.118	0.987	model1_4gcnA1.pdb.gz
2	7v9bA	0.85	1.65	0.171	1.000	model1_7v9bA.pdb.gz
3	7y4iA1	0.85	1.33	0.197	0.947	model1_7y4iA1.pdb.gz
4	2o98B	0.85	1.73	0.145	1.000	model1_2o98B.pdb.gz
5	2q7fA	0.81	1.82	0.149	0.921	model1_2q7fA.pdb.gz
6	2gw1A1	0.80	1.45	0.149	0.921	model1_2gw1A1.pdb.gz
7	1elwA	0.79	1.45	0.194	0.895	model1_1elwA.pdb.gz
8	1w3bA3	0.78	1.42	0.149	0.882	model1_1w3bA3.pdb.gz
9	1wao11	0.78	1.74	0.097	0.934	model1_1wao11.pdb.gz
10	2kc7A	0.76	1.31	0.159	0.855	model1_2kc7A.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:0071704	0.82	organic substance metabolic process
GO:0044260	0.81	cellular macromolecule metabolic process
GO:0044238	0.81	primary metabolic process
GO:0016043	0.81	cellular component organization
GO:0006996	0.80	organelle organization
GO:0090304	0.79	nucleic acid metabolic process
GO:0007005	0.79	mitochondrion organization
GO:0006259	0.77	DNA metabolic process
GO:0006281	0.74	DNA repair
GO:0022402	0.55	cell cycle process
GO:0000075	0.53	cell cycle checkpoint
GO:0036297	0.51	interstrand cross-link repair

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:0016020	0.88	membrane
GO:0043232	0.87	intracellular non-membrane-bounded organelle
GO:0005886	0.87	plasma membrane
GO:0005737	0.86	cytoplasm
GO:0005730	0.86	nucleolus
GO:0032991	0.65	macromolecular complex
GO:0043234	0.64	protein complex
GO:0043227	0.64	membrane-bounded organelle
GO:0043231	0.63	intracellular membrane-bounded organelle
GO:0044444	0.62	cytoplasmic part
GO:0044451	0.57	nucleoplasm part
GO:0043240	0.55	Fanconi anaemia nuclear complex
GO:0005739	0.52	mitochondrion
GO:0005654	0.52	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	0.168	1tjcA	0.554	2.40	0.145	0.724	1.14.11.2	13,28,34,53
2	0.060	1tqgA	0.634	1.97	0.066	0.737	2.7.13.3	10,44
3	0.060	2vn7A	0.645	3.00	0.079	1.000	3.2.1.3	NA
4	0.060	2pziA	0.669	2.55	0.082	0.908	2.7.11.1	NA
5	0.060	2ct8A	0.659	2.44	0.074	0.882	6.1.1.10	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	0.17	2br9A	0.852	1.65	0.171	1.000	0.41	III	complex1.pdb.gz	15,16,41,44,45,48,51,52
2	0.10	3fp2A	0.800	2.12	0.107	0.987	0.50	III	complex2.pdb.gz	11,15,18
3	0.06	3axyC	0.705	3.14	0.053	0.974	0.40	III	complex3.pdb.gz	9,12,18,19,42,45,46,49,53
4	0.04	2b05E	0.676	2.51	0.056	0.947	0.44	III	complex4.pdb.gz	14,15,18,42,45,49,53
5	0.04	1hz40	0.822	1.96	0.160	0.974	0.53	III	complex5.pdb.gz	22,26,46,49,54

	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.