D-I-TASSER P15538-D1

D-I-TASSER results for P15538-D1

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

Input Sequence in FASTA format

>P15538 (90 residues)
MALRAKAEVCMAVPWLSLQRAQALGTRAARVPRTVLPFEAMPRRPGNRWLRLLQIWREQG
YEDLHLEVHQTFQELGPIFRYDLGGAGMVC

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MALRAKAEVCMAVPWLSLQRAQALGTRAARVPRTVLPFEAMPRRPGNRWLRLLQIWREQGYEDLHLEVHQTFQELGPIFRYDLGGAGMVC
Prediction	CCCHCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHCCCCCSCC
Confidence	962101013423752113564434656666888988977689999973789999999858679999999999984980133249862139
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MALRAKAEVCMAVPWLSLQRAQALGTRAARVPRTVLPFEAMPRRPGNRWLRLLQIWREQGYEDLHLEVHQTFQELGPIFRYDLGGAGMVC
Prediction	743444343224333331551443454444467334325401745744012003013652354124313530662110123534646428
	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

CCCHCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHCCCCCSCC
MALRAKAEVCMAVPWLSLQRAQALGTRAARVPRTVLPFEAMPRRPGNRWLRLLQIWREQGYEDLHLEVHQTFQELGPIFRYDLGGAGMVC

3k9vA

0.25

0.16

4.83

1.25

HHsearch

---------------------------------ETRNVTDLPGPTNWPLLSLLEIFWKGGLKKQHDTLAEYHKKYGQIFRMKLGSFDSVH

3n9yA

0.43

0.26

7.50

1.15

CNFpred

------------------------------------PFNEIPSPGDNGWLNLYHFWRETGTHKVHLHHVQNFQKYGPIYREKLGNVESVY

3fksG

0.04

0.03

1.74

1.00

DEthreader

KEVEMRLKSIKNIEKITKTMKIVASTRLSKAKASAKDEAEQ---ELIVAIVTIKLS-----INGIG-PTQESALA-----IFYNEPSAMA

3na0A

0.41

0.26

7.52

0.96

SPARKS-K

----------------------------------PRPFNEIPSPGDNGWLNLYHFWRETGTHKVHLHHVQNFQKYGPIYREKLGNVESVY

4k0fA2

0.11

0.10

3.62

0.74

MapAlign

LSHFLALPLAQRISLIIIIPFIY---NIVWQLLYSLRKDRPPLVFYIPWVGSAVVYGM----KPYEFFEECQKKYGDIFSFVLLGRVMTV

4k0fA2

0.13

0.12

4.26

0.77

CEthreader

NIGLSHFLALPLAQRISLIIIIPFIYNIVWQLLYSLRKDRPPLVYWIPWVGSAVVYGM----KPYEFFEECQKKYGDIFSFVLLGRVMTV

3na0A

0.41

0.26

7.52

0.98

MUSTER

----------------------------------PRPFNEIPSPGDNGWLNLYHFWRETGTHKVHLHHVQNFQKYGPIYREKLGNVESVY

3na0A

0.41

0.26

7.52

1.19

HHsearch

----------------------------------PRPFNEIPSPGDNGWLNLYHFWRETGTHKVHLHHVQNFQKYGPIYREKLGNVESVY

3k9vA

0.25

0.16

4.83

0.77

FFAS-3D

---------------------------------ETRNVTDLPGPTNWPLLGLLEIFWKGGLKKQHDTLAEYHKKYGQIFRMKLGSFDSVH

1mkmB

0.06

2.50

0.55

EigenThreader

MSVSNAYKYMVVLEEKGFVLRKVEGEQSIPMVSRYSTASGKSILAFVPEKELKEYLKIVTITNPRVLKRELEKIRKRGGVPIFNGYPGVS

(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	0.5096

(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	4dvqA	0.55	1.84	0.877	0.633	model1_4dvqA.pdb.gz
2	7m8iA	0.53	1.61	0.523	0.600	model1_7m8iA.pdb.gz
3	7eg1B	0.52	3.88	0.095	0.878	model1_7eg1B.pdb.gz
4	3k9vA	0.50	2.28	0.196	0.589	model1_3k9vA.pdb.gz
5	6ncyA	0.50	4.01	0.049	0.900	model1_6ncyA.pdb.gz
6	6j3qA	0.50	3.94	0.073	0.878	model1_6j3qA.pdb.gz
7	4g32A	0.50	3.55	0.034	0.844	model1_4g32A.pdb.gz
8	7f38A	0.50	4.25	0.122	0.900	model1_7f38A.pdb.gz
9	8eduA	0.49	4.03	0.139	0.878	model1_8eduA.pdb.gz
10	5t98A	0.49	4.02	0.057	0.900	model1_5t98A.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:0016713	1.00	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen
GO:0008395	1.00	steroid hydroxylase activity
GO:1901363	0.95	heterocyclic compound binding
GO:0097159	0.95	organic cyclic compound binding
GO:0020037	0.94	heme binding
GO:0016709	0.79	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
GO:0004507	0.72	steroid 11-beta-monooxygenase activity
GO:0047783	0.69	corticosterone 18-monooxygenase 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:0044763	1.00	single-organism cellular process
GO:0044237	1.00	cellular metabolic process
GO:0008202	1.00	steroid metabolic process
GO:0065007	0.99	biological regulation
GO:0006700	0.98	C21-steroid hormone biosynthetic process
GO:0044281	0.95	small molecule metabolic process
GO:1901615	0.94	organic hydroxy compound metabolic process
GO:0042180	0.88	cellular ketone metabolic process
GO:0008211	0.85	glucocorticoid metabolic process
GO:0008203	0.84	cholesterol metabolic process
GO:0006704	0.83	glucocorticoid biosynthetic process
GO:0050896	0.80	response to stimulus
GO:0042221	0.79	response to chemical
GO:0034650	0.79	cortisol metabolic process
GO:1901700	0.78	response to oxygen-containing compound
GO:0051716	0.78	cellular response to stimulus
GO:0009725	0.78	response to hormone
GO:0071375	0.77	cellular response to peptide hormone stimulus
GO:0044550	0.77	secondary metabolite biosynthetic process
GO:1901617	0.72	organic hydroxy compound biosynthetic process
GO:0042181	0.72	ketone biosynthetic process
GO:0032342	0.71	aldosterone biosynthetic 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:0044444	1.00	cytoplasmic part
GO:0044446	0.95	intracellular organelle part
GO:0016020	0.95	membrane
GO:0005743	0.94	mitochondrial inner 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	2nq5A	0.447	4.38	0.080	0.867	2.1.1.14	NA
2	0.060	2fhbA	0.466	4.27	0.080	0.878	3.2.1.41	NA
3	0.060	2g25A	0.463	4.37	0.068	0.867	1.2.4.1	69
4	0.060	3mosA	0.454	4.06	0.039	0.844	2.2.1.1	NA
5	0.060	2d69A	0.446	4.47	0.022	0.889	4.1.1.39	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	3k9vA	0.499	2.28	0.196	0.589	0.10	HEM	complex1.pdb.gz	64,67,70,71,74
2	0.01	3hn3A	0.475	4.40	0.069	0.900	0.11	UUU	complex2.pdb.gz	54,56,78
3	0.01	1gk8A	0.477	4.35	0.047	0.900	0.14	CAP	complex3.pdb.gz	42,81,82,85
4	0.01	1bhgA	0.477	4.41	0.069	0.900	0.13	UUU	complex4.pdb.gz	49,53,61,64,75
5	0.01	1ir1A	0.480	4.31	0.047	0.911	0.14	CAP	complex5.pdb.gz	58,60,61,83,84
6	0.01	1rblA	0.470	4.37	0.034	0.922	0.15	UUU	complex6.pdb.gz	41,47,85

	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.