D-I-TASSER Q9H892-D3

D-I-TASSER results for Q9H892-D3

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

Input Sequence in FASTA format

>Q9H892 (116 residues)
SDKEANTAMGLFTDLALEERFQVWFQANLPGVLPALTGVLKTDPKVSSSSALCQCIAIMG
NLSAEPTTRRHMAACEEFGDGCLSLLARCEEDVDLFREVIYTLLGLMMNLCLQAPF

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| SDKEANTAMGLFTDLALEERFQVWFQANLPGVLPALTGVLKTDPKVSSSSALCQCIAIMGNLSAEPTTRRHMAACEEFGDGCLSLLARCEEDVDLFREVIYTLLGLMMNLCLQAPF
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
Confidence	96421019999999999999999999826468999999996286646889999999999310135899999973079999999999886427616789999999999999843899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| SDKEANTAMGLFTDLALEERFQVWFQANLPGVLPALTGVLKTDPKVSSSSALCQCIAIMGNLSAEPTTRRHMAACEEFGDGCLSLLARCEEDVDLFREVIYTLLGLMMNLCLQAPF
Prediction	86663540241044233464043214441440131023213444534535211300210241344441454146275024000400341476253135122330233121235358
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
SDKEANTAMGLFTDLALEERFQVWFQANLPGVLPALTGVLKTDPKVSSSSALCQCIAIMGNLSAEPTTRRHMAACEEFGDGCLSLLARCEEDVDLFREVIYTLLGLMMNLCLQAPF

6nmgA

0.09

3.30

1.33

DEthreader

PP-DMDVLLESLKCLCNLSTAQMLAAEAR--LVVRLAERVGLYRRSYPHEVQFFDLRLLFLLTARTDVRQQLFQELHGVRLLTDALELTLGLPAQETERAMEILKVLFNITFDSVK

3l6xA

0.13

4.49

0.78

SPARKS-K

DMDLTEVITGTLWNLSSHDSIKMEIVDHAHALTDEVIIPHSGWEHIEWESVLTNTAGCLRNVSSRSEARRKLRECDGLVDALIFIVQAEIGQKDSDSKLVENCVCLLRNLSYQVHR

3nowA

0.09

0.08

2.97

0.53

MapAlign

-QSCLYGVVTTFVNLCFINKRITVLANEG--ITTALCALA----KTESHNSQELIARVLNAVCGLKELRGKVVQE-GGVKALLRMA--LE----GTEKGKRHATQALARIGITINP

4k6jA

0.12

4.26

0.36

CEthreader

SLWGAERCLRVLESVTVNPENQSYLIAYKDSLIVSSAKALQHCEELAVEDCMRAIIGVLLNLTDNEWGSTKTGEQDGLIGTALNCVLQVPKYLEQRFDIRVLGLGLLINLVEYSAR

5xjgA3

0.15

0.14

4.62

0.69

MUSTER

HIRVQRNATGALLNMTHSEENRKELVNA--GAVPVLVSLLSST----DPDVQYYCTTALSNIAVDEANRKKLAQEPRLVSKLVSLMD----SPS--SRVKCQATLALRNLASDTSY

3l6xA3

0.19

0.18

5.86

0.96

HHsearch

DMDLTEVITGTLWNLSSHDSIKMEIV--DHA-LHALTDEVIIGEHIEWESVLTNTAGCLRNVSSESEARRKLRECDGLVDALIFIVQAEIGQKDSDSKLVENCVCLLRNLSYQVPA

3tt9A2

0.12

4.23

0.86

FFAS-3D

DLETKKQITGLLWNLSSNDKLKNLMITE--ALLTLTENIIIKANGLLDFDIFYNVTGCLRNMSSGADGRKAMRRCDGLIDSLVHYVRGTIADYQPDDKATENCVCILHNLSYQLE-

6q82A4

0.07

2.84

0.60

EigenThreader

DTDVLFRIETVLNTILVDSPWIKNIVDANKFFNQNVISVFQTGFQTLKLDFVRTSTTLIGTLAG--YFKQEPFQLNPYVEALFQGLHTCTNFTSSNDKLEVTVSTLCETCREELTP

5xgcA

0.13

0.12

4.18

0.77

CNFpred

NHQLQLAGALAIANFARNDANCIHMVD--NGIVEKLMDLLDRHVEDGNVTVQHAALSALRNLAIPVINKAKMLSA-GVTEAVLKFLKSE------MPPVQFKLLGTLRMLIDAQAE

6homA2

0.18

0.16

5.35

1.33

DEthreader

SELSKTVATFILQKILLDDTGLAYICQRFSHVAMILGKMVLQLSKEPSARLLKHVVRCYLRLSDNPRAREALRQC--LPDQLKD-TTFAQVLKDD-TTTKRWLAQLVKNLQE----

(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	0.7581

(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	6homA2	0.85	1.33	0.178	0.922	model1_6homA2.pdb.gz
2	3l6xA3	0.84	1.89	0.177	0.974	model1_3l6xA3.pdb.gz
3	2fv2C	0.84	1.36	0.178	0.922	model1_2fv2C.pdb.gz
4	1ho8A	0.83	1.75	0.108	0.948	model1_1ho8A.pdb.gz
5	2z6gA1	0.81	1.46	0.133	0.905	model1_2z6gA1.pdb.gz
6	4r0zA3	0.81	1.48	0.181	0.905	model1_4r0zA3.pdb.gz
7	3tt9A	0.80	2.00	0.156	0.931	model1_3tt9A.pdb.gz
8	4cv5B	0.78	1.81	0.095	0.905	model1_4cv5B.pdb.gz
9	1xm9A2	0.77	2.26	0.128	0.940	model1_1xm9A2.pdb.gz
10	1wa5B2	0.76	1.86	0.146	0.888	model1_1wa5B2.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:0004871	0.68	signal transducer activity
GO:0019899	0.60	enzyme binding
GO:0019902	0.59	phosphatase binding
GO:0019900	0.59	kinase binding
GO:0003712	0.59	transcription cofactor activity
GO:0098772	0.58	molecular function regulator
GO:0022892	0.57	substrate-specific transporter activity
GO:0086080	0.56	protein binding involved in heterotypic cell-cell adhesion
GO:0042277	0.56	peptide binding
GO:0016247	0.56	channel regulator activity
GO:0005048	0.55	signal sequence binding
GO:0045296	0.52	cadherin binding
GO:0044877	0.51	macromolecular complex binding
GO:0019215	0.50	intermediate filament 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	0.80	cellular process
GO:0044699	0.72	single-organism process
GO:0065007	0.68	biological regulation
GO:0050789	0.68	regulation of biological process
GO:0050794	0.67	regulation of cellular process
GO:0044763	0.67	single-organism cellular process
GO:0019222	0.63	regulation of metabolic process
GO:0080090	0.62	regulation of primary metabolic process
GO:0060255	0.62	regulation of macromolecule metabolic process
GO:0048518	0.62	positive regulation of biological process
GO:0031323	0.62	regulation of cellular metabolic process
GO:0051171	0.61	regulation of nitrogen compound metabolic process
GO:0050896	0.61	response to stimulus
GO:0048522	0.61	positive regulation of cellular process
GO:0044767	0.61	single-organism developmental process
GO:0031326	0.61	regulation of cellular biosynthetic process
GO:0010468	0.61	regulation of gene expression
GO:0007165	0.61	signal transduction
GO:0045893	0.60	positive regulation of transcription, DNA-templated
GO:0007166	0.60	cell surface receptor signaling pathway
GO:0006928	0.60	movement of cell or subcellular component
GO:0051302	0.59	regulation of cell division
GO:0051234	0.59	establishment of localization
GO:0048546	0.59	digestive tract morphogenesis
GO:0048519	0.59	negative regulation of biological process
GO:0032956	0.59	regulation of actin cytoskeleton organization
GO:0016055	0.59	Wnt signaling pathway
GO:0010171	0.59	body morphogenesis
GO:0007369	0.59	gastrulation
GO:0006950	0.59	response to stress
GO:0006357	0.59	regulation of transcription from RNA polymerase II promoter
GO:0001667	0.59	ameboidal-type cell migration
GO:0048856	0.58	anatomical structure development
GO:0048523	0.58	negative regulation of cellular process
GO:0045184	0.58	establishment of protein localization
GO:0016043	0.58	cellular component organization
GO:0008104	0.58	protein localization
GO:0006810	0.58	transport
GO:1902580	0.57	single-organism cellular localization
GO:0051239	0.57	regulation of multicellular organismal process
GO:0044802	0.57	single-organism membrane organization
GO:0042592	0.57	homeostatic process
GO:0034613	0.57	cellular protein localization
GO:0015031	0.57	protein transport
GO:2000146	0.56	negative regulation of cell motility
GO:1902582	0.56	single-organism intracellular transport
GO:1901888	0.56	regulation of cell junction assembly
GO:0098901	0.56	regulation of cardiac muscle cell action potential
GO:0090150	0.56	establishment of protein localization to membrane
GO:0086069	0.56	bundle of His cell to Purkinje myocyte communication
GO:0086042	0.56	cardiac muscle cell-cardiac muscle cell adhesion
GO:0086004	0.56	regulation of cardiac muscle cell contraction
GO:0086002	0.56	cardiac muscle cell action potential involved in contraction
GO:0072659	0.56	protein localization to plasma membrane
GO:0072594	0.56	establishment of protein localization to organelle
GO:0070830	0.56	bicellular tight junction assembly
GO:0055008	0.56	cardiac muscle tissue morphogenesis
GO:0048878	0.56	chemical homeostasis
GO:0045596	0.56	negative regulation of cell differentiation
GO:0043270	0.56	positive regulation of ion transport
GO:0042127	0.56	regulation of cell proliferation
GO:0034331	0.56	cell junction maintenance
GO:0034113	0.56	heterotypic cell-cell adhesion
GO:0033365	0.56	protein localization to organelle
GO:0030334	0.56	regulation of cell migration
GO:0010644	0.56	cell communication by electrical coupling
GO:0006886	0.56	intracellular protein transport
GO:0003229	0.56	ventricular cardiac muscle tissue development
GO:0003208	0.56	cardiac ventricle morphogenesis
GO:0002028	0.56	regulation of sodium ion transport
GO:0002027	0.56	regulation of heart rate
GO:1902593	0.55	single-organism nuclear import
GO:0044744	0.55	protein targeting to nucleus
GO:0017038	0.55	protein import
GO:0034333	0.52	adherens junction assembly
GO:1902589	0.51	single-organism organelle organization
GO:0045110	0.50	intermediate filament bundle assembly

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:0005813	1.00	centrosome

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	0.066	1tjcA	0.483	4.17	0.084	0.793	1.14.11.2	11,29
2	0.060	1gaiA	0.602	3.42	0.037	0.905	3.2.1.3	NA
3	0.060	1r76A	0.576	3.74	0.091	0.905	4.2.2.2	NA
4	0.060	1ft1B	0.605	3.67	0.063	0.914	2.5.1.58 2.5.1.-	NA
5	0.060	3gzkA	0.569	3.85	0.075	0.879	3.2.1.4	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	0.04	2gl7D	0.774	1.93	0.160	0.914	0.81	III	complex1.pdb.gz	36,39,43,55,59
2	0.04	2gl7A	0.816	1.41	0.133	0.905	0.87	III	complex2.pdb.gz	28,35,39,43,48,55,59,64
3	0.04	1t080	0.809	1.47	0.133	0.905	0.85	III	complex3.pdb.gz	61,64,98,102,103,105
4	0.04	1i7x0	0.774	2.26	0.152	0.966	0.75	III	complex4.pdb.gz	26,29,31,34,70,71,74,75
5	0.03	2bptA	0.755	2.58	0.080	0.966	0.86	III	complex5.pdb.gz	33,36,37,40,41,77,81
6	0.03	1bk6A	0.659	2.79	0.112	0.922	0.73	III	complex6.pdb.gz	15,57,61,64,65,102,105,109,113
7	0.03	1bk6B	0.659	2.79	0.112	0.922	0.70	III	complex7.pdb.gz	12,13,14,53,57,60,98,101,105

	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.