D-I-TASSER P62341-D2

D-I-TASSER results for P62341-D2

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

Input Sequence in FASTA format

>P62341 (69 residues)
QPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKVYACMMVFFLSNM
IENQCMSTG

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| QPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKVYACMMVFFLSNMIENQCMSTG
Prediction	CHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCC
Confidence	838999999999999999999983777889809999859999997269999999999999999860169
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| QPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKVYACMMVFFLSNMIENQCMSTG
Prediction	843332023114333333200112244114314343231133046331110133333133335314648
	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

CHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCC
QPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKVYACMMVFFLSNMIENQCMSTG

5jqzA

0.03

1.78

1.22

SPARKS-K

IEANSRMLKALIEIAKAIWKALWANSLLLEATSRGDTERMRQWAEEARKIYKEAEKIIDRADEIVEEAK

4zvcA

0.06

2.51

1.17

DEthreader

EEEKERQIASILSWEIDIIYKILDSDLGS--S-L-FNQTMTRNLNLRVKFLLQIRNTVSQIITLLRELF

3jacA

0.07

2.93

1.21

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG--GGGGGGGGGGGGGGGGGGGGGGG

3a0bC3

0.07

2.96

0.57

CEthreader

TILGFHLIVLGIGALLLVAKAMFFGGRVITNPTLDPRVIFGYLLNNLEDVVGGHIWIGLICIAGGIWHI

6me2A

0.09

3.35

0.47

EigenThreader

SWLASALACVLIFTIVVDILGNLLVILSVYRNKKLRNAGNIFVVSLAVANLVVAIYPYPLVLMSIFNNG

6uz0A1

0.12

0.10

3.61

0.50

FFAS-3D

HPVRRAAVKILVLFSMLIMCTILT--NCVFMAQHDPPPWTKYVE----YTFTAIYTFESLVKILAR---

6z3wD

0.10

3.74

0.94

SPARKS-K

LVEKRCWDIALGPLKQIPMNLFIMPTMMVCMMAWRPIQALMAISATQKFLQGLVYLIGNLMGLALAVYK

7d3uD

0.13

0.12

4.03

0.65

CNFpred

-----APRSILAFHMVSQIGYILLGVALFGPIG--LTAGIFYLLHHMIVKAALFLAIGAIEVRYGPRRL

3i9yA

0.05

0.04

2.09

1.17

DEthreader

MIEARQVSELSTRIISSVQMLSNAQERAG--R-F-LA-ELVT-VNQSQQLMQKTLELFSELNSTVNKLV

6m32A

0.09

3.35

0.79

MapAlign

QVVGGHLALLGVLGFIMGIYYISGIQVMVSLGIDTYTADLEAAGARLLGWAAFHFLVGSVLIFGGWRHW

(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	0.7343

(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	4zvcA	0.73	2.42	0.061	0.927	model1_4zvcA.pdb.gz
2	6rflC	0.70	2.57	0.059	0.899	model1_6rflC.pdb.gz
3	6ep3A2	0.70	3.07	0.043	0.927	model1_6ep3A2.pdb.gz
4	1dowA2	0.69	2.41	0.141	0.899	model1_1dowA2.pdb.gz
5	3dyjA	0.68	2.35	0.046	0.899	model1_3dyjA.pdb.gz
6	2a7kC	0.68	2.87	0.061	0.913	model1_2a7kC.pdb.gz
7	7b0yA2	0.68	1.74	0.036	0.768	model1_7b0yA2.pdb.gz
8	7cmgA	0.67	3.16	0.043	0.986	model1_7cmgA.pdb.gz
9	6ey0A	0.67	2.82	0.029	0.986	model1_6ey0A.pdb.gz
10	6pnjL	0.67	1.94	0.031	0.812	model1_6pnjL.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:0008430	1.00	selenium 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:0065007	1.00	biological regulation
GO:0009987	1.00	cellular process
GO:0008152	0.70	metabolic process
GO:0044699	0.68	single-organism process
GO:0071704	0.65	organic substance metabolic process
GO:0044237	0.64	cellular metabolic process
GO:0050789	0.62	regulation of biological process
GO:0044763	0.62	single-organism cellular process
GO:0050794	0.60	regulation of cellular process
GO:0043170	0.60	macromolecule metabolic process
GO:0044260	0.59	cellular macromolecule metabolic process
GO:0009058	0.57	biosynthetic process
GO:1901576	0.56	organic substance biosynthetic process
GO:0065008	0.56	regulation of biological quality
GO:0044249	0.55	cellular biosynthetic process
GO:0050896	0.54	response to stimulus
GO:0031323	0.54	regulation of cellular metabolic process
GO:0006810	0.54	transport
GO:0080090	0.53	regulation of primary metabolic process
GO:0060255	0.53	regulation of macromolecule metabolic process
GO:0042592	0.53	homeostatic process
GO:0034645	0.53	cellular macromolecule biosynthetic process
GO:0032502	0.53	developmental process
GO:2000112	0.52	regulation of cellular macromolecule biosynthetic process
GO:0071702	0.52	organic substance transport
GO:0051171	0.52	regulation of nitrogen compound metabolic process
GO:0048856	0.52	anatomical structure development
GO:0045184	0.52	establishment of protein localization
GO:0044767	0.52	single-organism developmental process
GO:0044765	0.52	single-organism transport
GO:0032268	0.52	regulation of cellular protein metabolic process
GO:0010468	0.52	regulation of gene expression
GO:0008104	0.52	protein localization
GO:0071705	0.51	nitrogen compound transport
GO:0051649	0.51	establishment of localization in cell
GO:0015031	0.51	protein transport
GO:0010817	0.51	regulation of hormone levels
GO:0010033	0.51	response to organic substance
GO:0001514	0.51	selenocysteine incorporation
GO:0042593	0.50	glucose homeostasis
GO:0035773	0.50	insulin secretion involved in cellular response to glucose stimulus
GO:0031016	0.50	pancreas development
GO:0009749	0.50	response to glucose

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	1.00	cell part
GO:0044424	0.92	intracellular part
GO:0044444	0.83	cytoplasmic part
GO:0043226	0.80	organelle
GO:0043229	0.79	intracellular organelle
GO:0043227	0.79	membrane-bounded organelle
GO:0043231	0.78	intracellular membrane-bounded organelle
GO:0005783	0.73	endoplasmic reticulum

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	0.066	2w5jA	0.519	2.24	0.062	0.710	3.6.3.14	NA
2	0.060	1itkB	0.585	3.68	0.072	0.957	1.11.1.6 1.11.1.7	NA
3	0.060	3kczA	0.593	2.12	0.047	0.768	2.4.2.30	NA
4	0.060	2q80A	0.584	2.70	0.066	0.855	2.5.1.29 2.5.1.10 2.5.1.1	20
5	0.060	1xqdA	0.470	3.70	0.086	0.783	1.7.99.7	28,32,39

	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:

Click to view	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	3gm1B	0.623	2.76	0.103	0.913	0.42	III	complex1.pdb.gz	26,29,37,38,41,45

	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.