D-I-TASSER P34998-D1

D-I-TASSER results for P34998-D1

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

Input Sequence in FASTA format

>P34998 (98 residues)
MGGHPQLRLVKALLLLGLNPVSASLQDQHCESLSLASNISGLQCNASVDLIGTCWPRSPA
GQLVVRPCPAFFYGVRYNTTNNGYRECLANGSWAARVN

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MGGHPQLRLVKALLLLGLNPVSASLQDQHCESLSLASNISGLQCNASVDLIGTCWPRSPAGQLVVRPCPAFFYGVRYNTTNNGYRECLANGSWAARVN
Prediction	CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCSCCCSSCCCCCCCCCSSSSCCCCCCCCCCCCCCCCSSSSSCCCCCSCCCCC
Confidence	99888752235566665506689999999986354689889988863256233379999981898269303067656788748998189995546789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MGGHPQLRLVKALLLLGLNPVSASLQDQHCESLSLASNISGLQCNASVDLIGTCWPRSPAGQLVVRPCPAFFYGVRYNTTNNGYRECLANGSWAARVN
Prediction	85543634414212121234224411442266254666454431343133211012614344404331243043343445430314036514656478
	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

CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCSCCCSSCCCCCCCCCSSSSCCCCCCCCCCCCCCCCSSSSSCCCCCSCCCCC
MGGHPQLRLVKALLLLGLNPVSASLQDQHCESLSLASNISGLQCNASVDLIGTCWPRSPAGQLVVRPCPAFFYGVRYNTTNNGYRECLANGSWAARVN

4a01A

0.11

0.09

3.35

1.00

DEthreader

ALATAIFSTVSFLLGGVTSLVSGFLGMKIATYANARTEAKGGKFARSGAVMGFL-------------AANLLFASLSSVILVCTTFAEIEIELKQISM

7lciR1

0.24

0.21

6.67

3.26

SPARKS-K

----------ATVSLWETVQKWREYRRQCQRSLTEDPPPATLFCNRTFDEY-ACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWLQKDL

6x18R

0.26

0.22

6.93

0.71

MapAlign

------VSLWETVQKW------REYRRQCQRSLTEDPPPATLFCNRTFDEY-ACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWLWRDL

6o9iC

0.23

0.19

6.07

0.66

CEthreader

---------------GELYQRWEHYGQECQKMLETTEPPSGLACNGSFDMY-ACWNYTAANTTARVSCPWYLPWFRQVSAGFVFRQCGSDGQWGSWRD

2qkhA

0.23

0.20

6.39

2.32

MUSTER

--GQT---------AGELYQRWERYRRECQETLAAAEPPSGLACNGSFDMY-VCWDYAAPNATARASCPWYLPWHHHVAAGFVLRQCGSDGQWGLWRD

2l27A

1.00

0.76

21.14

2.10

HHsearch

------------------------LQDQHCESLSLASNISGLQCNASVDLIGTCWPRSPAGQLVVRPCPAFFYGVRYNTTNNGYRECLANGSWAARVN

2qkhA

0.22

0.19

6.11

1.20

FFAS-3D

-----------GQTAGELYQRWERYRRECQETLAAAEPPSGLACNGSFDMY-VCWDYAAPNATARASCPWYLPWHHHVAAGFVLRQCGSDGQWGLWRD

3c5tA

0.20

0.18

5.86

0.70

EigenThreader

---------ATVSLWETVQKWREYRRQCQRSLTEDPPPATDLFCNRTFDEY-ACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWLRDLS

5nx2A

0.24

0.20

6.38

1.76

CNFpred

--TVSLWETVQKWR----------EYRRQCQRSLTEDPPPDLFCNRTFDEY-ACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWLQKDN

5hziA

0.07

0.06

2.55

1.00

DEthreader

LTPTERKRQGYIHELIVTEENYVNDLQLVTEFQKPLMELT-EKVAFVWLIMYFCQGAL--------LPMQRVRYAECSVNEGVSLEQAHQ-QLVFSVP

(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	0.583

(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	6o9iC	0.77	1.21	0.244	0.837	model1_6o9iC.pdb.gz
2	4ersA	0.76	1.79	0.250	0.857	model1_4ersA.pdb.gz
3	2qkhA	0.76	1.62	0.235	0.867	model1_2qkhA.pdb.gz
4	3c5tA	0.75	1.88	0.244	0.867	model1_3c5tA.pdb.gz
5	5vaiR	0.75	1.87	0.247	0.867	model1_5vaiR.pdb.gz
6	6fj3A1	0.68	2.31	0.289	0.847	model1_6fj3A1.pdb.gz
7	5ii0A	0.67	2.30	0.195	0.837	model1_5ii0A.pdb.gz
8	3n7pA	0.64	2.36	0.179	0.806	model1_3n7pA.pdb.gz
9	2x57A	0.62	2.91	0.198	0.837	model1_2x57A.pdb.gz
10	6e3yR1	0.60	2.26	0.181	0.735	model1_6e3yR1.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:0038023	1.00	signaling receptor activity
GO:0004930	0.90	G-protein coupled receptor 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	0.97	biological regulation
GO:0050789	0.96	regulation of biological process
GO:0050794	0.91	regulation of cellular process
GO:0044699	0.69	single-organism process
GO:0009987	0.67	cellular process
GO:0048518	0.65	positive regulation of biological process
GO:0050896	0.64	response to stimulus
GO:0048522	0.64	positive regulation of cellular process
GO:0065008	0.63	regulation of biological quality
GO:0044763	0.61	single-organism cellular process
GO:0019222	0.59	regulation of metabolic process
GO:0080090	0.58	regulation of primary metabolic process
GO:0031323	0.58	regulation of cellular metabolic process
GO:0042221	0.57	response to chemical
GO:0009893	0.57	positive regulation of metabolic process
GO:0009889	0.57	regulation of biosynthetic process
GO:0031326	0.56	regulation of cellular biosynthetic process
GO:0031325	0.56	positive regulation of cellular metabolic process
GO:0019220	0.56	regulation of phosphate metabolic process
GO:0010033	0.56	response to organic substance
GO:0007165	0.56	signal transduction
GO:0045937	0.55	positive regulation of phosphate metabolic process
GO:0031328	0.55	positive regulation of cellular biosynthetic process
GO:0009719	0.55	response to endogenous stimulus
GO:0051239	0.54	regulation of multicellular organismal process
GO:0009725	0.54	response to hormone
GO:1901700	0.52	response to oxygen-containing compound
GO:0051171	0.52	regulation of nitrogen compound metabolic process
GO:0007186	0.52	G-protein coupled receptor signaling pathway
GO:0065009	0.51	regulation of molecular function
GO:0023051	0.51	regulation of signaling
GO:0019219	0.51	regulation of nucleobase-containing compound metabolic process
GO:0010646	0.51	regulation of cell communication
GO:0010243	0.51	response to organonitrogen compound
GO:0045935	0.50	positive regulation of nucleobase-containing compound metabolic process
GO:0043435	0.50	response to corticotropin-releasing hormone

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:0044425	0.94	membrane part
GO:0031224	0.92	intrinsic component of membrane
GO:0044459	0.89	plasma membrane part
GO:0031226	0.87	intrinsic component of plasma membrane
GO:0016021	0.56	integral component of membrane
GO:0016020	0.52	membrane
GO:0044424	0.50	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	1t3tA	0.489	4.33	0.055	0.888	6.3.5.3	NA
2	0.060	1fo4A	0.456	4.63	0.046	0.867	1.17.1.4	NA
3	0.060	2e1qA	0.509	4.12	0.041	0.888	1.17.3.2 1.17.1.4	NA
4	0.060	1kb0A	0.435	4.55	0.057	0.837	1.1.99.-	NA
5	0.060	2ckjA	0.365	4.59	0.011	0.653	1.17.1.4 1.17.3.2	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	0.10	3iolA	0.756	1.83	0.256	0.867	1.03	III	complex1.pdb.gz	18,19,22,50,51,71,72,73,74,96
2	0.01	3eubS	0.331	4.94	0.000	0.684	0.65	FES	complex2.pdb.gz	58,60,61,62,88,91
3	0.01	2ckjD	0.358	4.38	0.041	0.694	0.68	FES	complex3.pdb.gz	57,58,59,61,62,64,87
4	0.01	2ckjC	0.386	4.63	0.068	0.725	0.64	FES	complex4.pdb.gz	53,55,65,66,67,82

	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.