D-I-TASSER Q969V5-D2

D-I-TASSER results for Q969V5-D2

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

Input Sequence in FASTA format

>Q969V5 (181 residues)
KVHLGEDLKSILSEAPGKCVPYAVIEGAVRSVKETLNSQFVENCKGVIQRLTLQEHKMVW
NRTTHLWNDCSKIIHQRTNTVPFDLVPHEDGVDVAVRVLKPLDSVDLGLETVYEKFHPSI
QSFTDVIGHYISGERPKGIQETEEMLKVGATLTGVGELVLDNNSVRLQPPKQGMQYYLSS
Q

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| KVHLGEDLKSILSEAPGKCVPYAVIEGAVRSVKETLNSQFVENCKGVIQRLTLQEHKMVWNRTTHLWNDCSKIIHQRTNTVPFDLVPHEDGVDVAVRVLKPLDSVDLGLETVYEKFHPSIQSFTDVIGHYISGERPKGIQETEEMLKVGATLTGVGELVLDNNSVRLQPPKQGMQYYLSSQ
Prediction	CCCCCHHHHHHHHHCCCCCSSSSSSSSSSSSCCCSSSCCCCCCCCSSSSSSSSSSSSHHHCCCCCCSSSCCCSSSSSSCSSCSSSSCCCCCCCSSSSSCCCCCCCCCCCSSSSSCSSSCCCCHHHHHHHHHCCCSSSCSSSSSSSCCCCCSSSSSSSSSSCCCSSSSSCCCCCCCSSSSCC
Confidence	9653458999998668981218999999997896275023588518999999653210121547700306012133411426799578888615999826742235762468340475788888985642114221011121110269945999999997299799866999974788379
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| KVHLGEDLKSILSEAPGKCVPYAVIEGAVRSVKETLNSQFVENCKGVIQRLTLQEHKMVWNRTTHLWNDCSKIIHQRTNTVPFDLVPHEDGVDVAVRVLKPLDSVDLGLETVYEKFHPSIQSFTDVIGHYISGERPKGIQETEEMLKVGATLTGVGELVLDNNSVRLQPPKQGMQYYLSSQ
Prediction	7353475045105627743010000203042474314143375030001303044133334634420454453145325302020144665341203124336256041420244044444312411222023433312430240044434010102012577414033167424010258
	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                 140                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHHHHHCCCCCSSSSSSSSSSSSCCCSSSCCCCCCCCSSSSSSSSSSSSHHHCCCCCCSSSCCCSSSSSSCSSCSSSSCCCCCCCSSSSSCCCCCCCCCCCSSSSSCSSSCCCCHHHHHHHHHCCCSSSCSSSSSSSCCCCCSSSSSSSSSSCCCSSSSSCCCCCCCSSSSCC
KVHLGEDLKSILSEAPGKCVPYAVIEGAVRSVKETLNSQFVENCKGVIQRLTLQEHKMVWNRTTHLWNDCSKIIHQRTNTVPFDLVPHEDGVDVAVRVLKPLDSVDLGLETVYEKFHPSIQSFTDVIGHYISGERPKGIQETEEMLKVGATLTGVGELVLDNNSVRLQPPKQGMQYYLSSQ

4me3A3

0.12

0.06

2.17

0.62

CEthreader

AYRIR-DIR------SANIGTLISVSGIVRK-----NTEVF---------------------------------PKFIDVQKVEIQED---PPQRITIITE--------------------------------------DDLAGLLYPGNRVIVDGILRTEQRRQGNIPLTEFFTYLYAIN

5svjA

0.06

0.04

1.99

0.82

EigenThreader

-----WTIGIINRVVKAYTAIESSVVTKVKGVSDYVTPPQGTSVFVIITKMIVTENQPEQCGPERGRCVNYVETPIMMEAENFGNFHPDKDPFCGWVCDLDKAWDQCGYNFRFAKYYKMEN-------------GSEYRTLLKAFGIR---FDVLVYGN-----AGKFN-----------I

4joiA

0.08

0.04

1.54

0.52

FFAS-3D

-----RDILDMKESRQVPGIKQVDVLGTVI------------------------------------------GVRERDAFYSYGVDDSTGVINCICW---------------------KKLQLKKLQETIEQKTK----------IEIGDTIRVRGSIRTYREEREIH-------------

6n2bA1

0.16

0.15

4.97

0.64

SPARKS-K

--SSWNDLFEYAVYSRGSFLPFTVRGGSIYSGER-IQTQ---GEFKAIGVNNLICKGPEVIVNGGGNSIEIKEIMYIQNK--LVFNGAPNTNPNTLNANKGLGGMELNGYKANEIYSDGEVQVKNYGNFEIGSIGIVKKLTVTTTIKSGATLYCDQLEVRNNGRVFIEA---GATLVTRAI

4z48A

0.09

0.08

2.96

0.85

CNFpred

------AGYDLAVRMDVDTSQDSYSEAVMSINR-----------GGKVLTRSFKTYSKHFGKDGKDEYSLIVFDRPAVNGTKYLVWSYRGEQDDDMWVYLPAESLVRRISSKFASFMRSDLSNEDIQNLDDV-DEYDYLLQGEENVD-GIDCYILERTPKKGKETQYSR----QVQWVRKD

5un7A

0.07

0.04

1.87

0.67

DEthreader

ERTPLC-AI--LK----QKAPQQYRIRAKLRSYKPRRLFQ-------SVKLVP---VHFVKNGILPLENSQIHHYQYVFVMTFTLDD----GTGVLEA--YL-MDSDKFFIPEVLMD----------------------DDLQSVIMFWLECFIKSYN-------QICY------QIFDTT

3h9vA

0.05

0.04

2.12

0.79

MapAlign

TQALVIAYVIYVFVYNKGYQDTDTVLSVTKVK-GIALTKTERIWFFVLTNMIITQTCAESYSASVKTCEVCPLEKPPLLAFTVLIKNNFNFNKRNPIFR-LGDIVGEAGGYNFRFAKYY----------KNSDGTETRTLIKGYGIRFDVMVFGQAGKFNI-IPTLLNIGAGLALLGLVNV

4xfvA

0.11

0.10

3.78

0.49

MUSTER

RQNIQNDEFGLAHEFTIKFFYPLCLSLSKVEEKKYLLAIGGTNVNVFIASFILSDSGIEKCRVVAELEGHE----DWVKSLAFRHQETPGDQDRYIRLWRIRINDLILSNKQYKFQIDDELRVGINFEALIMGHD--DWISSLQWHESRLQLLAATA----DTSLMVWEPDSGIWVCSLRL

4g2sA

0.11

0.06

2.01

0.54

HHsearch

------------------------------------------------------PYIVRL-------------LNSSLNGCEFPLLTG----RTLFVV-GQSDAPDIPA---DSFFIPLDHGGVNFEIQVDTDEIILEGNSESRSVQLNTPIQVGEL------LILIRPES--EPW-----

5odnA

0.16

0.08

2.77

0.54

CEthreader

--------------AMARGVNKVILIGNLGDD--------------PELRYT----------------------GSGTAVCNMSLATNETNTEWHDVVA-----------------------------------WGRLGEICNEYLDKGSQVYFEGKLQTRSWEDRDNNTRYSTEVKAQEM

(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	0.6455

(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	5dofA	0.44	2.76	0.083	0.530	model1_5dofA.pdb.gz
2	3kf8A	0.42	3.88	0.119	0.558	model1_3kf8A.pdb.gz
3	5un7A	0.41	4.88	0.157	0.663	model1_5un7A.pdb.gz
4	6ns0A1	0.41	3.33	0.132	0.519	model1_6ns0A1.pdb.gz
5	2i0qA	0.41	4.35	0.076	0.613	model1_2i0qA.pdb.gz
6	5lilA	0.41	5.23	0.053	0.691	model1_5lilA.pdb.gz
7	5f9yA	0.41	5.55	0.040	0.729	model1_5f9yA.pdb.gz
8	1slqA	0.41	5.74	0.046	0.740	model1_1slqA.pdb.gz
9	1s40A	0.40	3.68	0.099	0.541	model1_1s40A.pdb.gz
10	1bbuA1	0.40	3.72	0.102	0.536	model1_1bbuA1.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:0004842	1.00	ubiquitin-protein transferase activity
GO:0042802	0.93	identical protein binding
GO:0004871	0.93	signal transducer 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:0051128	1.00	regulation of cellular component organization
GO:0048522	1.00	positive regulation of cellular process
GO:0016567	1.00	protein ubiquitination
GO:0051646	0.93	mitochondrion localization
GO:0043123	0.93	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0030308	0.93	negative regulation of cell growth
GO:0006919	0.93	activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0000266	0.93	mitochondrial fission
GO:0044699	0.75	single-organism process
GO:0010821	0.73	regulation of mitochondrion organization
GO:0044763	0.72	single-organism cellular process
GO:1902589	0.67	single-organism organelle organization
GO:0050896	0.67	response to stimulus
GO:2001233	0.66	regulation of apoptotic signaling pathway
GO:1902532	0.66	negative regulation of intracellular signal transduction
GO:0080135	0.66	regulation of cellular response to stress
GO:0070887	0.66	cellular response to chemical stimulus
GO:0051239	0.66	regulation of multicellular organismal process
GO:0046902	0.66	regulation of mitochondrial membrane permeability
GO:0045088	0.66	regulation of innate immune response
GO:0032879	0.66	regulation of localization
GO:0010033	0.66	response to organic substance
GO:0001934	0.66	positive regulation of protein phosphorylation
GO:1901028	0.65	regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway
GO:0071650	0.65	negative regulation of chemokine (C-C motif) ligand 5 production
GO:0071360	0.65	cellular response to exogenous dsRNA
GO:0060339	0.65	negative regulation of type I interferon-mediated signaling pathway
GO:0051898	0.65	negative regulation of protein kinase B signaling
GO:0050689	0.65	negative regulation of defense response to virus by host
GO:0007257	0.65	activation of JUN kinase activity
GO:0022603	0.52	regulation of anatomical structure morphogenesis
GO:0090141	0.51	positive regulation of mitochondrial fission

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:0044446	1.00	intracellular organelle part
GO:0044444	1.00	cytoplasmic part
GO:0043231	1.00	intracellular membrane-bounded organelle
GO:0044429	0.84	mitochondrial part
GO:0016021	0.83	integral component of membrane
GO:0031307	0.82	integral component of mitochondrial outer membrane
GO:0005777	0.82	peroxisome
GO:0044428	0.56	nuclear part
GO:0005739	0.54	mitochondrion
GO:0005737	0.54	cytoplasm
GO:0005654	0.54	nucleoplasm

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	1ggmB	0.349	5.88	0.049	0.680	6.1.1.14	NA
2	0.060	3f9vA	0.377	3.20	0.077	0.481	3.-.-.-	NA
3	0.060	2oknA	0.376	5.70	0.052	0.707	3.4.13.9	NA
4	0.060	3e9hA	0.398	3.62	0.062	0.530	6.1.1.6	NA
5	0.060	2iw2A	0.370	5.81	0.059	0.718	3.4.13.9	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	0.01	1e22A	0.280	5.76	0.038	0.514	0.15	ACP	complex1.pdb.gz	88,157,166
2	0.01	1e24A	0.278	5.78	0.029	0.519	0.20	ATP	complex2.pdb.gz	30,47,48,149
3	0.01	2i461	0.370	3.56	0.055	0.503	0.24	III	complex3.pdb.gz	25,30,150,152,154
4	0.01	2b4h0	0.339	5.76	0.051	0.652	0.13	III	complex4.pdb.gz	45,46,47,48,49,76,148
5	0.01	1lylC	0.406	3.65	0.071	0.536	0.35	LYS	complex5.pdb.gz	153,155,177,179
6	0.01	3a74A	0.284	5.68	0.040	0.508	0.12	B4P	complex6.pdb.gz	24,26,165
7	0.01	2bhv0	0.379	5.17	0.078	0.685	0.21	III	complex7.pdb.gz	75,76,77,78,106,108,109,111,113,132,134,141,145,146
8	0.01	1ibk4	0.136	3.62	0.063	0.193	0.24	III	complex8.pdb.gz	26,27,28,29,32
9	0.01	1ibk9	0.146	3.89	0.079	0.204	0.39	III	complex9.pdb.gz	107,109,151,152,153,154
10	0.01	1e1oA	0.279	5.66	0.008	0.508	0.11	LYS	complex10.pdb.gz	110,146,149

	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.