D-I-TASSER Q6ZMQ8-D9

D-I-TASSER results for Q6ZMQ8-D9

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

Input Sequence in FASTA format

>Q6ZMQ8 (78 residues)
CPSGLVPEPPEPQGPAKVRPGPSPSCSQFFLLTPVPLRSEGNSSEFQGPPGLLSGPAPQK
RMGGPGTPRAPLRLALPG

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| CPSGLVPEPPEPQGPAKVRPGPSPSCSQFFLLTPVPLRSEGNSSEFQGPPGLLSGPAPQKRMGGPGTPRAPLRLALPG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCC
Confidence	998888899988897778998998765335426777888888868689975556877355778999999850430689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| CPSGLVPEPPEPQGPAKVRPGPSPSCSQFFLLTPVPLRSEGNSSEFQGPPGLLSGPAPQKRMGGPGTPRAPLRLALPG
Prediction	767565563445554472443443444322213424346746455264344425354456445547344332333258
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCC
CPSGLVPEPPEPQGPAKVRPGPSPSCSQFFLLTPVPLRSEGNSSEFQGPPGLLSGPAPQKRMGGPGTPRAPLRLALPG

2w2bA

0.10

3.77

0.52

CEthreader

LTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANI

6fviA

0.06

2.73

0.60

EigenThreader

TKPPSTKVKPTTEPGETSLENHGTTDVKWHLSSLPYVKGVDESGDVFTYAAFISSHGTFLPRGRGDYAQFWDVECKEP

1clhA

0.17

0.13

4.23

0.30

FFAS-3D

-----------------RTADKDSATSQFFINVADNAFLDHGQRDFGYAVFKISQVPTHDVGPYQNVPSKPVVILLP-

3bogA

0.14

4.79

1.18

SPARKS-K

CKGADGAHGVGCPGTAGAAGSVGGPGCDGGHGGNGG-NGNPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADGAP

5czdA

0.06

0.01

0.55

0.22

CNFpred

--------------------------VVTHSFVRAPRERLDE------------------------------------

1uc6A

0.06

0.05

2.26

1.00

DEthreader

SV-KPDPPEVVARPLVTWQTPWDPESFPLKFFLRYRPL-----DQWQ-H--VELGH-TITDAYAKEYIIQVAAKDNEI

1ev11

0.01

1.35

0.61

MapAlign

ACVFYLEYKTGTKEDSNSFNNWDMEITVVITSSVLTHQIMYVPPGGPIPVSVDDYSWQTSTNPSIFWTETSVARIYFK

4nl6A

0.17

5.50

0.75

MUSTER

ESQVSTDESENSRSPGNKSDNIKPKSAPWNSFLPPPPPMPGPRLGPGKPGLKFNGPPPPPPPPPPHLLSCWLPPFPSG

3al0B

0.17

0.10

3.36

0.43

HHsearch

----MRYRPVILEIHVQ-----LSTKTKAFCSCPAD--VF---------------------ELPPNTAICPVCTGQPG

1ee8A

0.14

0.13

4.37

0.51

CEthreader

LAEGRRILEVDRRGKFLLFALEGGVELVAHLGMTGGFR-------LEPTPHTRAALVLEGRTLYFHDPRRFGRLFGVR

(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	0.6069

(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	4r4xA2	0.59	3.24	0.093	0.949	model1_4r4xA2.pdb.gz
2	7chkA	0.59	3.08	0.067	0.962	model1_7chkA.pdb.gz
3	2v5yA	0.59	3.03	0.070	0.910	model1_2v5yA.pdb.gz
4	1cfbA2	0.58	2.89	0.044	0.859	model1_1cfbA2.pdb.gz
5	1x4xA	0.56	2.97	0.164	0.846	model1_1x4xA.pdb.gz
6	1tdqA	0.54	3.31	0.060	0.859	model1_1tdqA.pdb.gz
7	1uemA	0.54	3.39	0.029	0.885	model1_1uemA.pdb.gz
8	1x5zA	0.54	3.26	0.118	0.872	model1_1x5zA.pdb.gz
9	1qr4A1	0.54	3.15	0.109	0.821	model1_1qr4A1.pdb.gz
10	2crzA	0.53	3.49	0.088	0.872	model1_2crzA.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:0003824	0.49	catalytic activity
GO:0016740	0.46	transferase activity
GO:0016301	0.44	kinase activity
GO:0004672	0.43	protein kinase activity
GO:0004713	0.38	protein tyrosine kinase activity
GO:1901363	0.33	heterocyclic compound binding
GO:0097159	0.33	organic cyclic compound binding
GO:0035639	0.31	purine ribonucleoside triphosphate binding
GO:0032555	0.31	purine ribonucleotide binding
GO:0032550	0.31	purine ribonucleoside 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:0009987	0.94	cellular process
GO:0044699	0.93	single-organism process
GO:0044763	0.92	single-organism cellular process
GO:0065007	0.88	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.86	regulation of cellular process
GO:0044767	0.83	single-organism developmental process
GO:0007165	0.78	signal transduction
GO:0048856	0.77	anatomical structure development
GO:0048523	0.76	negative regulation of cellular process
GO:0071704	0.75	organic substance metabolic process
GO:0044237	0.75	cellular metabolic process
GO:0010977	0.75	negative regulation of neuron projection development
GO:0010771	0.75	negative regulation of cell morphogenesis involved in differentiation
GO:0044260	0.74	cellular macromolecule metabolic process
GO:0044238	0.74	primary metabolic process
GO:0035556	0.72	intracellular signal transduction
GO:0006796	0.72	phosphate-containing compound metabolic process
GO:0006464	0.72	cellular protein modification process
GO:0007264	0.71	small GTPase mediated signal transduction
GO:0006468	0.71	protein phosphorylation
GO:0061387	0.70	regulation of extent of cell growth
GO:0050771	0.70	negative regulation of axonogenesis
GO:0048640	0.70	negative regulation of developmental growth
GO:0046777	0.70	protein autophosphorylation
GO:0030308	0.70	negative regulation of cell growth
GO:0018108	0.70	peptidyl-tyrosine phosphorylation
GO:0008219	0.70	cell death
GO:0051402	0.69	neuron apoptotic process
GO:0038083	0.69	peptidyl-tyrosine autophosphorylation
GO:0032482	0.69	Rab protein signal transduction
GO:0030517	0.69	negative regulation of axon extension
GO:0007420	0.69	brain development

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	0.99	intracellular part
GO:0043226	0.93	organelle
GO:0043229	0.91	intracellular organelle
GO:0044444	0.86	cytoplasmic part
GO:0043227	0.86	membrane-bounded organelle
GO:0043231	0.81	intracellular membrane-bounded organelle
GO:0097458	0.78	neuron part
GO:0048471	0.74	perinuclear region of cytoplasm
GO:0044463	0.73	cell projection part
GO:0016020	0.73	membrane
GO:0005768	0.70	endosome
GO:0055037	0.69	recycling endosome
GO:0044295	0.69	axonal growth cone
GO:0005783	0.69	endoplasmic reticulum
GO:0044425	0.62	membrane part
GO:0031224	0.53	intrinsic component of membrane
GO:0016021	0.52	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	2i74A	0.505	3.83	0.027	0.962	3.5.1.52	NA
2	0.060	1novC	0.523	3.66	0.053	0.962	3.4.23.44	7
3	0.060	2dlhA	0.525	3.29	0.027	0.846	3.1.3.48	71
4	0.060	2mev1	0.522	3.84	0.027	0.936	3.6.1.15	NA
5	0.060	2ac1A	0.530	3.50	0.041	0.936	3.2.1.26	8

	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	3besR	0.567	3.40	0.042	0.897	0.47	UUU	complex1.pdb.gz	32,34,48
2	0.01	2b5i6	0.552	3.42	0.053	0.897	0.45	III	complex2.pdb.gz	29,30,48,53,54,55,76
3	0.01	3fcsC	0.528	3.66	0.042	0.885	0.41	IMD	complex3.pdb.gz	30,32,33,50,51

	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.