D-I-TASSER P13164-D1

D-I-TASSER results for P13164-D1

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

Input Sequence in FASTA format

>P13164 (125 residues)
MHKEEHEVAVLGPPPSTILPRSTVINIHSETSVPDHVVWSLFNTLFLNWCCLGFIAFAYS
VKSRDRKMVGDVTGAQAYASTAKCLNIWALILGILMTIGFILLLVFGSVTVYHIMLQIIQ
EKRGY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MHKEEHEVAVLGPPPSTILPRSTVINIHSETSVPDHVVWSLFNTLFLNWCCLGFIAFAYSVKSRDRKMVGDVTGAQAYASTAKCLNIWALILGILMTIGFILLLVFGSVTVYHIMLQIIQEKRGY
Prediction	CCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCSSHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence	97211155257999999998751551489999997332489999985212453999999987535566089899999999888999999999999999999999999999999999852432799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MHKEEHEVAVLGPPPSTILPRSTVINIHSETSVPDHVVWSLFNTLFLNWCCLGFIAFAYSVKSRDRKMVGDVTGAQAYASTAKCLNIWALILGILMTIGFILLLVFGSVTVYHIMLQIIQEKRGY
Prediction	74666462544442554443442334344744343100000000313333220000112024145244433362046104303210121133133333333333322333334203533674675
	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

CCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCSSHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
MHKEEHEVAVLGPPPSTILPRSTVINIHSETSVPDHVVWSLFNTLFLNWCCLGFIAFAYSVKSRDRKMVGDVTGAQAYASTAKCLNIWALILGILMTIGFILLLVFGSVTVYHIMLQIIQEKRGY

3qa8A

0.10

3.80

1.17

DEthreader

EFVGTL-YLAVDYFGAFILSILSVMNMIFGTSNLLNTELSKKKNSMTSCVQALVDKMMALQDSVDLQRNIQLSKTVVCKRKALELSPKVKEVMNLMREDEKIVVRRQEKRQQELWNLLKIACSKR

6vq6b

0.06

2.73

0.66

CEthreader

YTIFDLGFRFDVAWFLTETSPFMWSNLGIGLAISLSVVGAAWGIYITGSIIFCEAVAIYGIIMAIVISNMAFGAGLTVGLSNLFCGVCVGIVGSGAALADAQNPSLFVKILIVEIFGSAIGLFGV

6ig5A2

0.06

2.50

0.67

EigenThreader

GLDPDAIAADLGFSDNSVDATAA--RDFAAEAAFVFAMIAVDLSRLAEHDSWARGKSGRLIGNLAGLLATLKEPVFDSVAQLELLLPAMAGLVASREVLGSVSAGRVAEQLNAIGEAAERLRRQL

6n3qA1

0.11

0.09

3.21

0.67

FFAS-3D

-------------PEVIAPER--------KVPYNQKLIWTGVSLLIFTLLELGVSPIITSSMIFQFLQPESKQDRELFQIAQKVCAIILILGQALVVVLLLIFQLMFASLIVMLLDELLSKGYGL

6w2wA2

0.05

2.18

0.88

SPARKS-K

----------ENEAAKECLKAVRAALEAALLALLLLAKHPGSQAAQDAVQLATAALRAVEAACQLAKQYPNSDIAKKCIKAASEAAEEASKAAEEAQR----KARDEIKEASQKAEEVKERCERA

5oqtA

0.14

0.09

2.99

0.71

CNFpred

-----------------------------------LVLSFILSGLACVFAALCYAEFASTVPVS-------------GSAYTYSYATFGELIAWILGWDLILEYGVASSAVAVGWSGYFQGLLSG

5ebzA

0.07

0.06

2.63

1.17

DEthreader

------------LQIILRKAEHYGLKDYLFGQRAMLLRYNANLTKMKNLEDQIMSLHAEIMLQKSPYGRVELFGHLSKLLGCKQKIIDLLPKVEVALSNIKEADNTVMFMQGKRQKEIWHLLKIA

4o9uB

0.06

2.72

0.71

MapAlign

-MGNFALILLALLLGSVVAWWAAVRVAMTDMPQAINGMGGGAAATIALGGLIGSVAFTGSLIAFAKLQPIGGGDMPVAISFYNAFTGMAVGFEGFANPALMVAGTLVGAAGTLLTVLMARAMNRS

2r9rB3

0.14

0.11

3.84

0.68

MUSTER

---------------------SKGLQILGQTLKASMRELGLLIFFLFIGVILFSSAVYFAEADERDSQFPSIPDAFWWAVVSMTTTIGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRET--

6rz6A2

0.13

0.10

3.31

0.50

HHsearch

---------------------------LNLYKIAKLQTMNYIALVVGCLLPFFTLSICYLLIIRVLLKVEDNAYIQKYLVSHRKALTTIIITLIIFFLCFLPYHTLRTVLTTW--------KVGL

(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	0.6748

(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	3qa8A	0.68	3.40	0.064	0.992	model1_3qa8A.pdb.gz
2	6d03E	0.64	3.19	0.036	0.872	model1_6d03E.pdb.gz
3	4e40A	0.64	2.69	0.018	0.808	model1_4e40A.pdb.gz
4	6rjwA	0.64	2.59	0.063	0.784	model1_6rjwA.pdb.gz
5	6at7B	0.63	3.51	0.048	0.920	model1_6at7B.pdb.gz
6	5ebzA3	0.63	3.22	0.051	0.912	model1_5ebzA3.pdb.gz
7	1w27A	0.62	3.78	0.065	0.864	model1_1w27A.pdb.gz
8	4hpqC	0.61	3.31	0.056	0.840	model1_4hpqC.pdb.gz
9	1y2mB	0.58	3.55	0.082	0.832	model1_1y2mB.pdb.gz
10	2q13A	0.57	3.13	0.055	0.784	model1_2q13A.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:0004871	0.62	signal transducer activity
GO:0005057	0.59	receptor signaling protein 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:0065007	0.82	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0050794	0.79	regulation of cellular process
GO:0009987	0.78	cellular process
GO:0050896	0.69	response to stimulus
GO:0048523	0.65	negative regulation of cellular process
GO:0016032	0.65	viral process
GO:0010033	0.65	response to organic substance
GO:0035455	0.64	response to interferon-alpha
GO:0009615	0.64	response to virus
GO:0046597	0.63	negative regulation of viral entry into host cell
GO:0045071	0.63	negative regulation of viral genome replication
GO:0035456	0.63	response to interferon-beta
GO:0034341	0.63	response to interferon-gamma
GO:0007165	0.62	signal transduction
GO:0019221	0.57	cytokine-mediated signaling pathway
GO:0002376	0.53	immune system process
GO:0060337	0.52	type I interferon signaling pathway
GO:0044699	0.50	single-organism 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:0044464	0.99	cell part
GO:0016020	0.95	membrane
GO:0005886	0.90	plasma membrane
GO:0044424	0.65	intracellular 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	1w27A	0.621	3.59	0.064	0.872	4.3.1.24	NA
2	0.060	1dofA	0.515	3.42	0.056	0.744	4.3.2.2	NA
3	0.060	1yfmA	0.517	2.80	0.048	0.656	4.2.1.2	NA
4	0.060	1ivhA	0.486	3.29	0.048	0.648	1.3.99.10	82
5	0.060	2bl2A	0.510	3.36	0.069	0.696	3.6.3.14	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	2q7mC	0.523	3.14	0.090	0.720	0.78	2CS	complex1.pdb.gz	61,63,64,65,67,76
2	0.01	2q7mB	0.487	3.30	0.088	0.704	0.73	2CS	complex2.pdb.gz	84,86,88,89,91,92
3	0.01	2q7mF	0.524	3.20	0.080	0.720	0.61	2CS	complex3.pdb.gz	71,73,74,75,77
4	0.01	2q7mA	0.464	3.12	0.088	0.640	0.62	2CS	complex4.pdb.gz	72,74,75,76,78,79

	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.