D-I-TASSER Q9BT40-D2

D-I-TASSER results for Q9BT40-D2

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

Input Sequence in FASTA format

>Q9BT40 (123 residues)
VSAPLIVLMPEDLWTVENDMMVSYSSTSDFPSSPWDWIGLYKVGLRDVNDYVSYAWVGDS
KVSCSDNLNQVYIDISNIPTTEDEFLLCYYSNSLRSVVGISRPFQIPPGSLREDPLGEAQ
PQI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VSAPLIVLMPEDLWTVENDMMVSYSSTSDFPSSPWDWIGLYKVGLRDVNDYVSYAWVGDSKVSCSDNLNQVYIDISNIPTTEDEFLLCYYSNSLRSVVGISRPFQIPPGSLREDPLGEAQPQI
Prediction	CCCCSSSSSCCCCSCCCCCSSSSSSSCCCCCCCCCCSSSSSSCCCCCHHHSSSSSSSCCCCCCCCCCCSSSSSSCCCCCCCCCSSSSSSSSCCCCSSSSSCCCSSSCCCCCCCCCCCCCCCCC
Confidence	998759983574053899779999957997468875489997256882126899995577667787618999850016888987999999989985999748858739982213355555789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VSAPLIVLMPEDLWTVENDMMVSYSSTSDFPSSPWDWIGLYKVGLRDVNDYVSYAWVGDSKVSCSDNLNQVYIDISNIPTTEDEFLLCYYSNSLRSVVGISRPFQIPPGSLREDPLGEAQPQI
Prediction	874220413247403373502030324551444443112114341531530201010446565656433203043630354743110001035442010204405044563764416665568
	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                 100                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCSSSSSCCCCSCCCCCSSSSSSSCCCCCCCCCCSSSSSSCCCCCHHHSSSSSSSCCCCCCCCCCCSSSSSSCCCCCCCCCSSSSSSSSCCCCSSSSSCCCSSSCCCCCCCCCCCCCCCCC
VSAPLIVLMPEDLWTVENDMMVSYSSTSDFPSSPWDWIGLYKVGLRDVNDYVSYAWVGDSKVSCSDNLNQVYIDISNIPTTEDEFLLCYYSNSLRSVVGISRPFQIPPGSLREDPLGEAQPQI

3vvvA

0.25

0.21

6.54

1.17

DEthreader

G-PSQVIFNVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWV-TL--PI-DKQQEVQFKAYYLPKDDEYYQFCYVDE-DGVVRGASIPFQFRPE--------------

3vvvA

0.24

0.21

6.58

2.08

SPARKS-K

-GPSQVIFNVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWVTLP----IDKQQEVQFKAYYLPKDDEYYQFCYVDEDGV-VRGASIPFQFRPENEED----------

3vvvA

0.25

0.21

6.54

0.61

MapAlign

--PSQVIFNVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWV----TLPIDKQQEVQFKAYYLPKDDEYYQFCYVDE-DGVVRGASIPFQFRPE--------------

3vvvA

0.24

0.21

6.58

0.59

CEthreader

-GPSQVIFNVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWV----TLPIDKQQEVQFKAYYLPKDDEYYQFCYVDED-GVVRGASIPFQFRPENEED----------

3vvvA

0.24

0.21

6.58

1.86

MUSTER

-GPSQVIFNVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWVTLP----IDKQQEVQFKAYYLPKDDEYYQFCYVDED-GVVRGASIPFQFRPENEED----------

3vvvA

0.22

0.20

6.14

4.43

HHsearch

-GPSQVIFNSVKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWVTLPID----KQQEVQFKAYYLPKDDEYYQFCYVDEDG-VVRGASIPFQFRPENEED----------

4nlhA

0.23

0.20

6.37

1.75

FFAS-3D

-SPAHVIFQNVKSYLPNAHLECHYTLTPYIHPHPKDWVGIFKVGWSTARDYYTFLWSPMHYVEGSTVNCVLAFQGYYLPNDDGEFYQFCYVTHKGEIRGASTPFQFRASS-------------

3vvvA

0.22

0.20

6.14

0.63

EigenThreader

-GPSQVIFNSVEKFYIPGGVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWV----TLPIDKQQEVQFKAYYLPKDDEYYQFCYVDED-GVVRGASIPFQFRPENEED----------

4nlhA

0.21

0.19

5.93

1.71

CNFpred

-SPAHVIFQNVKSYLPNAHLECHYTLTPYIHPHPKDWVGIFKVGWSTARDYYTFLWSPMPEHYVSTVNCVLAFQGYYLPNDDEFYQFCYVTHK-GEIRGASTPFQFRASS-------------

4nlhA

0.20

0.17

5.45

1.17

DEthreader

--PAHVIFQVAKSYLPNAHLECHYTLTPYIHPHPKDWVGIFKVGWSTARDYYTFLWS-P--MPEHYVNCVLAFQGYYLPNDGEFYQFCYVTH-KGEIRGASTPFQFR-AS-------------

(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	0.7873

(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	3vvvA	0.79	1.32	0.234	0.837	model1_3vvvA.pdb.gz
2	4nlhA	0.77	2.30	0.204	0.870	model1_4nlhA.pdb.gz
3	4fxgA	0.65	3.66	0.079	0.927	model1_4fxgA.pdb.gz
4	3x17B	0.64	3.45	0.083	0.878	model1_3x17B.pdb.gz
5	3zk4A	0.63	2.78	0.098	0.805	model1_3zk4A.pdb.gz
6	3prxB4	0.61	3.76	0.099	0.878	model1_3prxB4.pdb.gz
7	3hs0F2	0.58	3.10	0.091	0.789	model1_3hs0F2.pdb.gz
8	2p9rA	0.54	3.55	0.083	0.756	model1_2p9rA.pdb.gz
9	2pn5A	0.54	4.05	0.068	0.870	model1_2pn5A.pdb.gz
10	3gzkA1	0.54	2.13	0.087	0.650	model1_3gzkA1.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	0.95	catalytic activity
GO:0016787	0.90	hydrolase activity
GO:0016791	0.89	phosphatase activity
GO:0052745	0.88	inositol phosphate phosphatase activity
GO:0052866	0.82	phosphatidylinositol phosphate phosphatase activity
GO:0034485	0.81	phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity
GO:0004871	0.77	signal transducer activity
GO:0016312	0.75	inositol bisphosphate phosphatase activity
GO:0005000	0.75	vasopressin 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:0050794	0.96	regulation of cellular process
GO:0009987	0.91	cellular process
GO:0051128	0.89	regulation of cellular component organization
GO:0048518	0.84	positive regulation of biological process
GO:0044699	0.84	single-organism process
GO:0033043	0.84	regulation of organelle organization
GO:0048522	0.83	positive regulation of cellular process
GO:0008152	0.83	metabolic process
GO:0048519	0.82	negative regulation of biological process
GO:0048523	0.80	negative regulation of cellular process
GO:0044710	0.80	single-organism metabolic process
GO:0051239	0.79	regulation of multicellular organismal process
GO:0044237	0.79	cellular metabolic process
GO:0060255	0.78	regulation of macromolecule metabolic process
GO:0044763	0.78	single-organism cellular process
GO:0080090	0.77	regulation of primary metabolic process
GO:0031323	0.77	regulation of cellular metabolic process
GO:0006796	0.77	phosphate-containing compound metabolic process
GO:0071704	0.76	organic substance metabolic process
GO:0044238	0.76	primary metabolic process
GO:0007165	0.76	signal transduction
GO:0051129	0.75	negative regulation of cellular component organization
GO:0046488	0.74	phosphatidylinositol metabolic process
GO:0044092	0.73	negative regulation of molecular function
GO:0032269	0.73	negative regulation of cellular protein metabolic process
GO:0016311	0.73	dephosphorylation
GO:0006355	0.73	regulation of transcription, DNA-templated
GO:0001932	0.73	regulation of protein phosphorylation
GO:0051494	0.72	negative regulation of cytoskeleton organization
GO:0050896	0.72	response to stimulus
GO:0044419	0.72	interspecies interaction between organisms
GO:0044087	0.72	regulation of cellular component biogenesis
GO:0033137	0.72	negative regulation of peptidyl-serine phosphorylation
GO:0009966	0.72	regulation of signal transduction
GO:0051240	0.71	positive regulation of multicellular organismal process
GO:0034097	0.71	response to cytokine
GO:0016043	0.71	cellular component organization
GO:0006810	0.71	transport
GO:0065008	0.70	regulation of biological quality
GO:0046856	0.70	phosphatidylinositol dephosphorylation
GO:0044765	0.70	single-organism transport
GO:0032879	0.70	regulation of localization
GO:0032501	0.70	multicellular organismal process
GO:0031325	0.70	positive regulation of cellular metabolic process
GO:0010604	0.70	positive regulation of macromolecule metabolic process
GO:0006886	0.70	intracellular protein transport
GO:2001153	0.69	positive regulation of renal water transport
GO:2000466	0.69	negative regulation of glycogen (starch) synthase activity
GO:0097178	0.69	ruffle assembly
GO:0090315	0.69	negative regulation of protein targeting to membrane
GO:0072661	0.69	protein targeting to plasma membrane
GO:0071364	0.69	cellular response to epidermal growth factor stimulus
GO:0071356	0.69	cellular response to tumor necrosis factor
GO:0071320	0.69	cellular response to cAMP
GO:0051926	0.69	negative regulation of calcium ion transport
GO:0051898	0.69	negative regulation of protein kinase B signaling
GO:0051497	0.69	negative regulation of stress fiber assembly
GO:0046627	0.69	negative regulation of insulin receptor signaling pathway
GO:0045893	0.69	positive regulation of transcription, DNA-templated
GO:0045892	0.69	negative regulation of transcription, DNA-templated
GO:0045869	0.69	negative regulation of single stranded viral RNA replication via double stranded DNA intermediate
GO:0045719	0.69	negative regulation of glycogen biosynthetic process
GO:0043922	0.69	negative regulation by host of viral transcription
GO:0043407	0.69	negative regulation of MAP kinase activity
GO:0042593	0.69	glucose homeostasis
GO:0035810	0.69	positive regulation of urine volume
GO:0035305	0.69	negative regulation of dephosphorylation
GO:0032869	0.69	cellular response to insulin stimulus
GO:0010829	0.69	negative regulation of glucose transport
GO:0010801	0.69	negative regulation of peptidyl-threonine phosphorylation
GO:0007186	0.69	G-protein coupled receptor signaling pathway

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:0044444	0.96	cytoplasmic part
GO:0043227	0.88	membrane-bounded organelle
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0005829	0.84	cytosol
GO:0016020	0.82	membrane
GO:0005737	0.82	cytoplasm
GO:0042995	0.78	cell projection
GO:0001726	0.77	ruffle
GO:0044446	0.76	intracellular organelle part
GO:0097458	0.75	neuron part
GO:0044463	0.75	cell projection part
GO:0005886	0.75	plasma membrane
GO:0044425	0.73	membrane part
GO:0005634	0.72	nucleus
GO:0048471	0.71	perinuclear region of cytoplasm
GO:0005783	0.71	endoplasmic reticulum
GO:0044431	0.70	Golgi apparatus part
GO:0043005	0.69	neuron projection
GO:0032587	0.69	ruffle membrane
GO:0005802	0.69	trans-Golgi network

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	0.122	1k85A	0.489	3.24	0.096	0.675	3.2.1.14	26,41,97
2	0.066	2djmA	0.522	3.24	0.087	0.732	3.2.1.3	12,72
3	0.066	1zvhA	0.568	3.10	0.093	0.789	3.2.1.17	86,99
4	0.066	2dleA	0.477	3.82	0.072	0.724	3.1.3.48	57,99
5	0.066	1u2hA	0.467	3.60	0.066	0.699	2.7.11.1	23

	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	0.08	1op3M	0.605	3.31	0.106	0.846	0.60	MAN	complex1.pdb.gz	38,39,54,91,96,97
	2	0.02	1nolA	0.624	3.32	0.086	0.846	0.53	CA	complex2.pdb.gz	25,26,27,99

	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.