D-I-TASSER Q68DA7-D6

D-I-TASSER results for Q68DA7-D6

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

Input Sequence in FASTA format

>Q68DA7 (76 residues)
QFLHELAQIPNFAERAQCIIFRSRGQADGYSLEILPKLKDVKSRDNGINLVDYVVKYYLR
YYDQEAGTEKSVFPLP

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| QFLHELAQIPNFAERAQCIIFRSRGQADGYSLEILPKLKDVKSRDNGINLVDYVVKYYLRYYDQEAGTEKSVFPLP
Prediction	CHHHHHHCCCCHHHHHHHHHSSCCCCCCCCCSSSSHHHHSSSCCCCCCSHHHHHHHHHHHHCCCCCCCCCCCCCCC
Confidence	6378886098446734421010003566664353102220004689820899999999996742379654547899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| QFLHELAQIPNFAERAQCIIFRSRGQADGYSLEILPKLKDVKSRDNGINLVDYVVKYYLRYYDQEAGTEKSVFPLP
Prediction	7214414514414421200113333444224042144045244665432001200430154257745376242628
	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

CHHHHHHCCCCHHHHHHHHHSSCCCCCCCCCSSSSHHHHSSSCCCCCCSHHHHHHHHHHHHCCCCCCCCCCCCCCC
QFLHELAQIPNFAERAQCIIFRSRGQADGYSLEILPKLKDVKSRDNGINLVDYVVKYYLRYYDQEAGTEKSVFPLP

1v9dB2

0.18

5.97

1.06

SPARKS-K

AACEELRKSENFSSLLELTLLVGNAGAFGFNISFLCKLRDTKSADQKMTLLHFLAELCENDHPEVLKFPDELAHVE

1v9dB2

0.17

0.16

5.17

1.22

MUSTER

SLLELTLLVGNYMN-------SRNAGAFGFNISFLCKLRDTKSADQKMTLLHFLAELCENDHPEVLKFPDELAHVE

1v9dB

0.21

6.68

2.74

HHsearch

QFGVVMGTVPRLRPRLNAILFKLNAGAFGFNISFLCKLRDTKSADQKMTLLHFLAELCENDHPEVLKFPDELAHVE

1ux4A

0.21

6.68

1.09

CNFpred

KAVSALQESDNLRNVFNVILAVGNKQAQGFKLSTLQRLTFIKDTTNSMTFLNYVEKIVRLNYPSFNDFLSELEPVL

2gwcF

0.12

0.11

3.75

0.83

DEthreader

LTHQTCAVVWLCALPAFWVGLLDVLQVLLTAWPERLKLTPGL-----LKHVAEDVLKLAKDGLERRKV--GFLNAV

1v9dB

0.21

6.68

0.87

SPARKS-K

QFGVVMGTVPRLRPRLNAILFKLQFGAFGFNISFLCKLRDTKSADQKMTLLHFLAELCENDHPEVLKFPDELAHVE

5gquA

0.07

2.76

0.71

MapAlign

GFYSPTSRFGRPEDFMYFVDKCHENGIGVYFDGTHLYEHIGEHKEWGTLVFSFIREVNTLLVSRPVYDGGLGFNL-

4nrhB

0.04

2.04

0.59

CEthreader

KEGYHAYLDKDYAKSITVFRWLVFFNPFVSKF--WFSLGASLHMSEQYSQALHAYGVTAVLRDKDPYPHYYAYICY

1ux4A

0.22

0.20

6.24

1.22

MUSTER

NVFNVILAVGNFMND-------TSKQAQGFKLSTLQRLTFIKDTTNSMTFLNYVEKIVRLNYPSFNDFLSELEPVL

2z6eB

0.29

8.82

2.74

HHsearch

RFLFEMSRINHYQQRLQSLYFKKRGNAYGFKISSLNKIADTKSSDKNITLLHYLITIVENKYPSVLNLNEELRDIP

(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	0.5716

(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	1ux4A	0.60	3.06	0.132	0.868	model1_1ux4A.pdb.gz
2	4eahA	0.59	3.21	0.147	0.855	model1_4eahA.pdb.gz
3	2z6eB	0.57	2.89	0.133	0.829	model1_2z6eB.pdb.gz
4	1v9dB	0.55	3.46	0.133	0.855	model1_1v9dB.pdb.gz
5	3h2tA	0.44	3.73	0.069	0.750	model1_3h2tA.pdb.gz
6	3eg9A2	0.40	4.12	0.028	0.684	model1_3eg9A2.pdb.gz
7	4xdnA3	0.38	3.85	0.057	0.671	model1_4xdnA3.pdb.gz
8	1u19A	0.38	4.31	0.045	0.724	model1_1u19A.pdb.gz
9	4b63A1	0.38	4.39	0.030	0.763	model1_4b63A1.pdb.gz
10	4zhjA5	0.37	4.17	0.095	0.737	model1_4zhjA5.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:0008092	0.92	cytoskeletal protein binding
GO:0003779	0.58	actin 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:0044763	1.00	single-organism cellular process
GO:0032502	1.00	developmental process
GO:0016043	1.00	cellular component organization
GO:0050794	0.99	regulation of cellular process
GO:0048869	0.99	cellular developmental process
GO:0048856	0.99	anatomical structure development
GO:0044767	0.99	single-organism developmental process
GO:0051179	0.64	localization
GO:0022607	0.64	cellular component assembly
GO:0051641	0.62	cellular localization
GO:0048468	0.62	cell development
GO:0007015	0.62	actin filament organization
GO:0003006	0.62	developmental process involved in reproduction
GO:0048477	0.61	oogenesis
GO:0048518	0.55	positive regulation of biological process
GO:0006996	0.55	organelle organization
GO:1902589	0.54	single-organism organelle organization
GO:0080090	0.54	regulation of primary metabolic process
GO:0060255	0.54	regulation of macromolecule metabolic process
GO:0007010	0.54	cytoskeleton organization
GO:0006810	0.54	transport
GO:0048522	0.53	positive regulation of cellular process
GO:0048519	0.53	negative regulation of biological process
GO:0065008	0.52	regulation of biological quality
GO:0051246	0.52	regulation of protein metabolic process
GO:0050896	0.52	response to stimulus
GO:0048523	0.52	negative regulation of cellular process
GO:0006928	0.52	movement of cell or subcellular component
GO:1902578	0.51	single-organism localization
GO:0051716	0.51	cellular response to stimulus
GO:0051128	0.51	regulation of cellular component organization
GO:0046907	0.51	intracellular transport
GO:0042221	0.51	response to chemical
GO:0022402	0.51	cell cycle process
GO:0016192	0.51	vesicle-mediated transport
GO:0010605	0.51	negative regulation of macromolecule metabolic process
GO:0007018	0.51	microtubule-based movement
GO:0071456	0.50	cellular response to hypoxia
GO:0070649	0.50	formin-nucleated actin cable assembly
GO:0051758	0.50	homologous chromosome movement towards spindle pole involved in homologous chromosome segregation
GO:0051493	0.50	regulation of cytoskeleton organization
GO:0051295	0.50	establishment of meiotic spindle localization
GO:0043066	0.50	negative regulation of apoptotic process
GO:0042177	0.50	negative regulation of protein catabolic process
GO:0040038	0.50	polar body extrusion after meiotic divisions
GO:0006974	0.50	cellular response to DNA damage stimulus

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:0044424	1.00	intracellular part
GO:0005737	0.99	cytoplasm
GO:0043226	0.92	organelle
GO:0043229	0.91	intracellular organelle
GO:0005856	0.89	cytoskeleton
GO:0044444	0.74	cytoplasmic part
GO:0043227	0.71	membrane-bounded organelle
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0044422	0.63	organelle part
GO:0044446	0.62	intracellular organelle part
GO:0016020	0.62	membrane
GO:0005938	0.62	cell cortex
GO:0005829	0.56	cytosol
GO:0044428	0.53	nuclear part
GO:0031090	0.53	organelle membrane
GO:0030659	0.50	cytoplasmic vesicle membrane
GO:0015629	0.50	actin cytoskeleton
GO:0005730	0.50	nucleolus

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	1t7nA	0.478	3.92	0.055	0.882	2.3.1.7	NA
2	0.060	2zueA	0.499	3.86	0.106	0.842	6.1.1.19	NA
3	0.060	3d4jB	0.458	3.55	0.092	0.803	4.1.1.33	49
4	0.060	2e8iA	0.445	3.82	0.083	0.842	3.5.1.46	NA
5	0.060	2cb1A	0.475	3.79	0.068	0.882	4.2.99.10	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:

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	0.01	1innB	0.495	3.93	0.113	0.882	0.44	MET	complex1.pdb.gz	21,24,54
	2	0.01	1j6xB	0.447	3.88	0.044	0.816	0.42	MET	complex2.pdb.gz	22,53,54

	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.