D-I-TASSER O43462-D2

D-I-TASSER results for O43462-D2

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

Input Sequence in FASTA format

>O43462 (169 residues)
VLITEVAEDSPAIGPRGLFVGDLVTHLQDCPVTNVQDWNECLDTIAYEPQIGYCISASTL
QQLSFPVRAYKRLDGSTECCNNHSLTDVCFSYRNNFNKRLHTCLPARKAVEATQVCRTNK
DCKKSSSSSFCIIPSLETHTRLIKVKHPPQIDMLYVGHPLHLHYTVSIT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| VLITEVAEDSPAIGPRGLFVGDLVTHLQDCPVTNVQDWNECLDTIAYEPQIGYCISASTLQQLSFPVRAYKRLDGSTECCNNHSLTDVCFSYRNNFNKRLHTCLPARKAVEATQVCRTNKDCKKSSSSSFCIIPSLETHTRLIKVKHPPQIDMLYVGHPLHLHYTVSIT
Prediction	CSSSSSCCCCCCCCCCCCCCCCSSSSSCCCSCCCHHHHHHHHHHHHCCCCCCSSCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCSSCCCCCSSSCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCSSSSSSSCCCCCSSSSCCHHHHSSSSSSC
Confidence	7897735999876877888885899977707036215999998775189983222888865325556554344782126789997632268715888764131461206247862148987787888854776457897279999947999779975879813444619
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| VLITEVAEDSPAIGPRGLFVGDLVTHLQDCPVTNVQDWNECLDTIAYEPQIGYCISASTLQQLSFPVRAYKRLDGSTECCNNHSLTDVCFSYRNNFNKRLHTCLPARKAVEATQVCRTNKDCKKSSSSSFCIIPSLETHTRLIKVKHPPQIDMLYVGHPLHLHYTVSIT
Prediction	3403403761304244404443103303604053472034004413644440211346204424552533444523240037634330003236536443211030242254444143465046444422002012654131020326754200000314203430528
	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

CSSSSSCCCCCCCCCCCCCCCCSSSSSCCCSCCCHHHHHHHHHHHHCCCCCCSSCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCSSCCCCCSSSCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCSSSSSSSCCCCCSSSSCCHHHHSSSSSSC
VLITEVAEDSPAIGPRGLFVGDLVTHLQDCPVTNVQDWNECLDTIAYEPQIGYCISASTLQQLSFPVRAYKRLDGSTECCNNHSLTDVCFSYRNNFNKRLHTCLPARKAVEATQVCRTNKDCKKSSSSSFCIIPSLETHTRLIKVKHPPQIDMLYVGHPLHLHYTVSIT

3wklA

0.09

3.36

0.59

CEthreader

VVVGYVQRDSIAQ-KIGIKPGDKIIKINGYEVRTWEDLRDALIRLSLDGVKETTLFLERNGEVLHLTIKVPNVQKGEELGIAPLVKPVVGGVKKGSPAD------QVGIKPGDLILEVNGKKINTWYELVEEVRKSQGKAIKLKILRNGKMIEKELIPAKDPKTGTYFI

2xhcA

0.05

0.04

1.90

0.62

EigenThreader

KKWYILTMSGYEEKVKENIKNLVGRIVIPEEVAT--------------SPSERLLSP------KASAGIEVKQ--GLPLSKNEEYIRMKKVQTPDGEQDVYYIPLDVFDRDRIKAKVSS-------TRKEIRIYKISGPFGVIKEIDPERQELKVNVT-------IF-G

6z05A4

0.20

0.07

2.08

0.58

FFAS-3D

VLVDSVKEKSK-GKNSGFQEGDIIIGVGQSEIKNLKDLEQALKQVNKKEFTKVWV------------------------------------------------------------------------------------------------------------------

3rleA

0.10

0.09

3.32

0.94

SPARKS-K

YHVLRVQENSPGHRA-GLEPFDFIVSINGSRLNKNDTLKDLLKANVEKPVKLIYSSKT--LELETSVTPSNLWGGQGLLFDGANENVWHVLEVESGLRPHSDYIDLFSLIETHE----------AKPLKLYVYNTDTDNCREVIITPNSAWGGEGSLGCGIGYGYLHRI

5xdyA

0.18

0.05

1.54

1.10

CNFpred

AQVANVKAGSPAQ-KGGILENDVIVKVGNRAVADSDEFVVAVRQLA---------------------------------------------------------------------------------------------------------------------------

6cy1A

0.05

0.04

1.71

0.83

DEthreader

------ESDKGLEKSSQSFFDKVVLIVGTKIIIIREEISGLLLEN-PHAG-----VVGVNGVKTIGLAHFKEGLKDVVI------------LSKRMVAPEVLLVLDGSTGNAFEAKQ-F--TAA----TEVTALA----V--L---A--RGGVVIIFNGTEFVDSFFKK

2xkxA

0.09

3.34

0.82

MapAlign

IYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEMHEDAVAALKNTEDIPREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFIGELRKGDQILSVNGVDL-R-NASHEQAAI--------ALKNAGQTVTIIAQYKPRFGDVLHVIDADEEWWQARRVHSDSETDDIGFI

2fylB

0.17

0.08

2.72

0.74

MUSTER

-----------------------------------------------SART--CPPNQFSCASGRCIPISWTCDLDDDCGDRSDESASC-AYPTCFPLTQFTCNNGR-CININWRCDNDNDCGDNSDEAGCSH------------------------------------

6z05A

0.17

0.15

4.89

0.80

HHsearch

ALITDVQKGSSADE-AGLKRGDLVTKVNNKVIKSPIDLKNYIGTLE----IGQKISLSYERDGENKASFILKGEKENPK-GVQSIDGLSLRNLDPRL-KDRLQIPKDGVLV-DS-VKEKSKGKN---------SGFQEGDIIIGVGQSKKEFTKVWVYRNGFATLLVLK

1u3bA

0.07

0.06

2.46

0.56

CEthreader

VIIANMMHGGPAEKSGKLNIGDQIMSINGTSLVGLSTCQSIIKGLKNQRCPPVTTVLIRRPDLRYQLGFSVQNGIICSLMRGGIAERGGVRVG-----HRIIEINGQSVVATPHEKIVHILSNAVGEIHMKTMPAAMYRLLTAQEQPVYI-------------------

(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	0.605

(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	4ak9A	0.45	5.38	0.059	0.787	model1_4ak9A.pdb.gz
2	2qy9A	0.45	5.19	0.054	0.769	model1_2qy9A.pdb.gz
3	2q9bA	0.45	5.24	0.040	0.769	model1_2q9bA.pdb.gz
4	1a6eA	0.44	5.37	0.066	0.775	model1_1a6eA.pdb.gz
5	4k7gB	0.44	5.22	0.050	0.751	model1_4k7gB.pdb.gz
6	1we3F	0.38	6.02	0.061	0.734	model1_1we3F.pdb.gz
7	2ynjA2	0.38	5.61	0.052	0.686	model1_2ynjA2.pdb.gz
8	1qzwA	0.36	6.23	0.034	0.722	model1_1qzwA.pdb.gz
9	1vmaA1	0.35	4.49	0.082	0.544	model1_1vmaA1.pdb.gz
10	2iy3A	0.35	6.19	0.063	0.710	model1_2iy3A.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:0004222	1.00	metalloendopeptidase 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:0071704	1.00	organic substance metabolic process
GO:0044238	1.00	primary metabolic process
GO:0043170	0.98	macromolecule metabolic process
GO:0031293	0.97	membrane protein intracellular domain proteolysis
GO:0009987	0.96	cellular process
GO:0050794	0.95	regulation of cellular process
GO:2000112	0.94	regulation of cellular macromolecule biosynthetic process
GO:0080090	0.94	regulation of primary metabolic process
GO:0051716	0.94	cellular response to stimulus
GO:0051171	0.94	regulation of nitrogen compound metabolic process
GO:0048522	0.94	positive regulation of cellular process
GO:0044699	0.94	single-organism process
GO:0010468	0.94	regulation of gene expression
GO:0006950	0.94	response to stress
GO:1990440	0.93	positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress
GO:0051091	0.93	positive regulation of sequence-specific DNA binding transcription factor activity
GO:0044710	0.92	single-organism metabolic process
GO:0006629	0.91	lipid metabolic process
GO:1901360	0.89	organic cyclic compound metabolic process
GO:0044281	0.89	small molecule metabolic process
GO:0036500	0.88	ATF6-mediated unfolded protein response
GO:0008203	0.88	cholesterol metabolic 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:0005737	1.00	cytoplasm
GO:0044425	0.91	membrane part
GO:0016021	0.90	integral component of 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	1cefA	0.387	5.12	0.032	0.657	3.4.16.4	NA
2	0.060	3fsnB	0.395	5.02	0.095	0.675	5.2.1.7	NA
3	0.060	3hm7B	0.387	5.77	0.014	0.698	3.5.2.5	NA
4	0.060	2cseW	0.402	5.50	0.071	0.710	3.6.4.13	NA
5	0.060	3hz3A	0.385	5.95	0.059	0.722	2.4.1.5	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	0.01	2j65A	0.391	5.23	0.065	0.686	0.12	UDP	complex1.pdb.gz	41,51,52
2	0.01	2j65A	0.391	5.23	0.065	0.686	0.19	MYR	complex2.pdb.gz	111,154,157
3	0.01	2go3A	0.394	5.16	0.058	0.686	0.30	MYR	complex3.pdb.gz	10,17,18,19
4	0.01	3dbmA	0.325	5.65	0.068	0.586	0.20	HO2	complex4.pdb.gz	10,14,20
5	0.01	2o3zA	0.393	5.17	0.051	0.686	0.20	AI7	complex5.pdb.gz	17,22,24
6	0.01	2q9bA	0.445	5.24	0.040	0.769	0.16	GNP	complex6.pdb.gz	4,10,155,157,158
7	0.01	2j65B	0.393	5.18	0.058	0.686	0.30	MYR	complex7.pdb.gz	3,5,14,17,22
8	0.01	2cnwD	0.364	5.63	0.045	0.680	0.11	UUU	complex8.pdb.gz	14,16,17,163,166
9	0.01	1yhcB	0.392	5.13	0.072	0.680	0.20	PAM	complex9.pdb.gz	145,157,163
10	0.01	2jt2A	0.396	5.07	0.065	0.686	0.15	C90	complex10.pdb.gz	13,14,37,38,41

	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.