D-I-TASSER P34925-D2

D-I-TASSER results for P34925-D2

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

Input Sequence in FASTA format

>P34925 (37 residues)
TTSTRVFYISVGVCCAVIFLVAIILAVLHLHSMKRIE

Predicted Secondary Structure

Sequence	20 \| TTSTRVFYISVGVCCAVIFLVAIILAVLHLHSMKRIE
Prediction	CCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	9734899998115689999999999999986543059
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 \| TTSTRVFYISVGVCCAVIFLVAIILAVLHLHSMKRIE
Prediction	8553312313233112313331332121314526648
	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

                   |

SS
Seq

CCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHHHHHCC
TTSTRVFYISVGVCCAVIFLVAIILAVLHLHSMKRIE

4jppA

0.08

3.19

1.67

DEthreader

KMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQV

3dl8C

0.11

3.86

1.46

SPARKS-K

KATISVIIFSLAIGVYLWILDLTFTKIISFILSLR--

2l6wA

0.19

6.11

1.46

MUSTER

SLPFKVVVISAILALVVLTIISLIILIMLWQKKPRYE

6b3rA

0.08

3.19

1.67

DEthreader

ALYNAANLKSINFHRQIEEKSLAQLKRQMKRIRAKQE

1mztA

0.19

0.16

5.24

1.17

SPARKS-K

LQASATEYIGYAWAMVVVIVGATIGIKLFKKF-----

4jq6A

0.03

1.73

0.89

MapAlign

VPVKWKTSLTVAGLVTGVAFWHYLYMRGVWIYAGETP

3mktA2

0.08

3.19

0.62

CEthreader

RGYKDMTAIFHRTFISYWVLGLPTGYILGMTNWLTEQ

1iijA

0.15

0.14

4.57

1.39

MUSTER

QRASPVTFIIATVVGVLLFLILVVVVGILIKRRR---

2kluA

0.08

3.19

0.56

HHsearch

VPRGSMALIVLGGVAGLLLFIGLGIFFSVRSRHRRRQ

4x5mA

0.00

0.81

0.28

FFAS-3D

---SDFAVLIANIVTLFLAAPVLVITLINRRKK----

(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	0.6113

(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	6z9lA	0.92	0.58	0.081	1.000	model1_6z9lA.pdb.gz
2	1vw1A	0.91	1.14	0.054	1.000	model1_1vw1A.pdb.gz
3	6wbpA	0.91	0.96	0.000	1.000	model1_6wbpA.pdb.gz
4	6wcjB	0.91	0.98	0.054	1.000	model1_6wcjB.pdb.gz
5	6ux2A	0.91	1.25	0.054	1.000	model1_6ux2A.pdb.gz
6	6yvuB	0.91	0.69	0.108	1.000	model1_6yvuB.pdb.gz
7	7apkG	0.91	0.99	0.054	1.000	model1_7apkG.pdb.gz
8	5h07D	0.91	1.16	0.054	1.000	model1_5h07D.pdb.gz
9	6lthN2	0.91	1.00	0.000	1.000	model1_6lthN2.pdb.gz
10	2ieqB	0.91	0.99	0.135	1.000	model1_2ieqB.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:0017147	0.87	Wnt-protein binding
GO:0005102	0.56	receptor binding
GO:0005109	0.50	frizzled 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:0044767	1.00	single-organism developmental process
GO:0035567	1.00	non-canonical Wnt signaling pathway
GO:0009653	1.00	anatomical structure morphogenesis
GO:0006928	1.00	movement of cell or subcellular component
GO:0040011	0.79	locomotion
GO:0048856	0.67	anatomical structure development
GO:0048518	0.67	positive regulation of biological process
GO:0080090	0.66	regulation of primary metabolic process
GO:0060255	0.66	regulation of macromolecule metabolic process
GO:0048522	0.66	positive regulation of cellular process
GO:0031323	0.66	regulation of cellular metabolic process
GO:0048583	0.65	regulation of response to stimulus
GO:0031325	0.65	positive regulation of cellular metabolic process
GO:0023051	0.65	regulation of signaling
GO:0010646	0.65	regulation of cell communication
GO:0010604	0.65	positive regulation of macromolecule metabolic process
GO:0051239	0.64	regulation of multicellular organismal process
GO:0048869	0.64	cellular developmental process
GO:0016043	0.64	cellular component organization
GO:0009966	0.64	regulation of signal transduction
GO:0001932	0.64	regulation of protein phosphorylation
GO:2000026	0.63	regulation of multicellular organismal development
GO:1902533	0.63	positive regulation of intracellular signal transduction
GO:0043408	0.63	regulation of MAPK cascade
GO:0022603	0.63	regulation of anatomical structure morphogenesis
GO:0001934	0.63	positive regulation of protein phosphorylation
GO:1904953	0.62	Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation
GO:1904938	0.62	planar cell polarity pathway involved in axon guidance
GO:0048519	0.62	negative regulation of biological process
GO:0043410	0.62	positive regulation of MAPK cascade
GO:0022038	0.62	corpus callosum development
GO:0007411	0.62	axon guidance
GO:0007409	0.62	axonogenesis
GO:0048523	0.61	negative regulation of cellular process
GO:0032879	0.60	regulation of localization

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:0016020	1.00	membrane
GO:0005886	0.82	plasma membrane
GO:0044424	0.75	intracellular part
GO:0043229	0.68	intracellular organelle
GO:0043227	0.67	membrane-bounded organelle
GO:0043231	0.66	intracellular membrane-bounded organelle
GO:0005634	0.65	nucleus
GO:0005737	0.62	cytoplasm

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	0.124	1z8yN	0.735	1.04	0.086	0.946	3.4.21.90	NA
2	0.096	1ybzA	0.791	1.25	0.081	1.000	5.4.99.5	NA
3	0.094	1qleD	0.700	1.42	0.111	0.946	1.9.3.1	NA
4	0.092	1wt6B	0.851	1.12	0.054	1.000	2.7.11.1	NA
5	0.091	2w1aD	0.784	1.25	0.027	1.000	5.4.99.5	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:

No Binding sites was predicted

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

	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.