D-I-TASSER Q96DX4-D4

D-I-TASSER results for Q96DX4-D4

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

Input Sequence in FASTA format

>Q96DX4 (263 residues)
NLSSIRAMLNSNDVSEYLKISPHGLEARCDASSFESVRCTFCVDAGVWYYEVTVVTSGVM
QIGWATRDSKFLNHEGYGIGDDEYSCAYDGCRQLIWYNARSKPHIHPCWKEGDTVGFLLD
LNEKQMIFFLNGNQLPPEKQVFSSTVSGFFAAASFMSYQQCEFNFGAKPFKYPPSMKFST
FNDYAFLTAEEKIILPRHRRLALLKQVSIRENCCSLCCDEVADTQLKPCGHSDLCMDCAL
QLETCPLCRKEIVSRIRQISHIS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| NLSSIRAMLNSNDVSEYLKISPHGLEARCDASSFESVRCTFCVDAGVWYYEVTVVTSGVMQIGWATRDSKFLNHEGYGIGDDEYSCAYDGCRQLIWYNARSKPHIHPCWKEGDTVGFLLDLNEKQMIFFLNGNQLPPEKQVFSSTVSGFFAAASFMSYQQCEFNFGAKPFKYPPSMKFSTFNDYAFLTAEEKIILPRHRRLALLKQVSIRENCCSLCCDEVADTQLKPCGHSDLCMDCALQLETCPLCRKEIVSRIRQISHIS
Prediction	CCCCCCSSCCHHHCCCCSSSSCCCSSSSSCCCCSSSSSSCCCSCCCSSSSSSSSSCCCCSSSSSSCCCCCCCCCCCCCCCCCCCSSSSSCCCCSSSSCCCCCCCCCCCCCCCCSSSSSSSCCCCSSSSSSCCSSCCCCCCCCCCCCCCCCCCSSCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCHSHHHHHHHHHCHCCCCCHHHHHHHHHHHCCC
Confidence	99976304571108886799599509997576156887364505885999999960990699987289987768886668877527886899759957988877788755894999999637736899989956133221222357885331322677059999830233456764322223343222221122332100011212222345543224666646986178721357877884218798745887724641589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| NLSSIRAMLNSNDVSEYLKISPHGLEARCDASSFESVRCTFCVDAGVWYYEVTVVTSGVMQIGWATRDSKFLNHEGYGIGDDEYSCAYDGCRQLIWYNARSKPHIHPCWKEGDTVGFLLDLNEKQMIFFLNGNQLPPEKQVFSSTVSGFFAAASFMSYQQCEFNFGAKPFKYPPSMKFSTFNDYAFLTAEEKIILPRHRRLALLKQVSIRENCCSLCCDEVADTQLKPCGHSDLCMDCALQLETCPLCRKEIVSRIRQISHIS
Prediction	83752312003513243030263303031444312000022205411000000034622000000144041444433331224100001144131112344454135404431000000203332010121243034333322234442020223343230201122333222222222222223222322222322232122223233333233202544120000002000002420530450100144045104414538
	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                 200                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCSSCCHHHCCCCSSSSCCCSSSSSCCCCSSSSSSCCCSCCCSSSSSSSSSCCCCSSSSSSCCCCCCCCCCCCCCCCCCCSSSSSCCCCSSSSCCCCCCCCCCCCCCCCSSSSSSSCCCCSSSSSSCCSSCCCCCCCCCCCCCCCCCCSSCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCHSHHHHHHHHHCHCCCCCHHHHHHHHHHHCCC
NLSSIRAMLNSNDVSEYLKISPHGLEARCDASSFESVRCTFCVDAGVWYYEVTVVTSGVMQIGWATRDSKFLNHEGYGIGDDEYSCAYDGCRQLIWYNARSKPHIHPCWKEGDTVGFLLDLNEKQMIFFLNGNQLPPEKQVFSSTVSGFFAAASFMSYQQCEFNFGAKPFKYPPSMKFSTFNDYAFLTAEEKIILPRHRRLALLKQVSIRENCCSLCCDEVADTQLKPCGHSDLCMDCALQLETCPLCRKEIVSRIRQISHIS

3tojA

0.22

0.15

4.79

1.00

DEthreader

LCLYERVLLALHDRAPQLKISDDRLTVVGE-KGYSMVRASHGVRKGAWYFEITVDEMTAARLGWSQPLGNLQ----APLGYDKFSYSWRSKKGTKFHQSIGKHY-SSGYGQGDVLGFYINLPSSEIIFYKNGVNQGV--AYKDIFEGVYFPAISLYKSCTVSINFGPCFKYPPKDLTYRPMSDMGWG----------------------------------------------------------------------------

4xw3A

0.23

0.16

5.13

2.35

SPARKS-K

-SVLNKWQMNPYDRGSAFAIGSDGLCCQSREVEWHGCRATKGLMKGKHYYEVSCHDQGLCRVGWSTMQASLD------LGTDKFGFGFGG-TGKKSHN-KQFDNYGEEFTMHDTIGCYLDIDKGHVKFSKNGKDLGLAFEIPPHMKQALFPACVLKN-AELKFNFGEEEFKFPPKDGFVALSKA----PDGYIVKSQHSGNA-------------------------------------------------------------

6chgB

0.21

0.15

4.83

1.32

MapAlign

-----KSSINLMDRSDKLAFSLDDHSVSVSENCWRSVRSDVCMKEGKIYWEVEVKNVSHIRCGISRREASTE----TPVGCDFYGYSIRDKGLQVIHEGRLHTLKPHEMQAGDRIGFLLTLPNSSFEVFVNGVSH---GIAFEGLTLGYYATLSSFQGGTASIITEAMELKFLPKDDIKTLNDIY-----------------------------------------------NEQIASDIVWDLIDEI---------------

6chgB

0.20

0.15

4.86

0.85

CEthreader

TDYFDKSSINLMDRSDKLAFSLDDHSVSVSENCWRSVRSDVCMKEGKIYWEVEVKNVSHIRCGISRREASTET----PVGCDFYGYSIRDKGLQVIHEGRLHTVLKHEMQAGDRIGFLLTLPSLSFEVFVNGVSHGIAFEGLTPFRLGYYATLSSFQGGTASIITEAMELKFLPKDDIKTLNDIYNEQIASDIVWDLIDEI--------------------------------------------------------------

4xw3A

0.22

0.16

4.92

1.52

MUSTER

-SVLNKWQMNPYDRGSAFAIGSDGLCCQSEVKEWHGCRATKGLMKGKHYYEVSCHDQGLCRVGWSTMQASLD------LGTDKFGFGFGG-TGKKSHNK-QFDNYGEEFTMHDTIGCYLDIDKGHVKFSKNGKDLGLAFEIPPHKNQALFPACVL-KNAELKFNFGEEEFKFPPKDGFVALSKAP---------------DGYIVKSQHSGNA--------------------------------------------------

6pwvD

0.22

0.17

5.51

2.23

HHsearch

ACLYERVLLALHDRAPQLKISDDRLTVVG-EKGYSMVRASHGVRKGAWYFEITVDEDTAARLGWSQPLGNLQAP----LGYDKFSYSWRSKKGTKFHQSI-GKHYSSGYGQGDVLGFYINLPEDEIIFYKNGVNQGVAYKDI--FEGVYFPAISLYKSCTVSINFGPC-FKYPPKLTYRPMSDMGW---GAVVEHTLADVLYHVETEVDGRRSPPWEP---------------------------------------------

4xw3A

0.21

0.15

4.70

1.59

FFAS-3D

--VLNKWQMNPYDRGSAFAIGSDGLCCQSREKEWHGCRATKGLMKGKHYYEVSCHDQGLCRVGWSTMQAS------LDLGTDKFGFGFGGTG--KKSHNKQFDNYGEEFTMHDTIGCYLDIDKGHVKFSKNGKDLGLAFEIPPHKNQALFPACVLK-NAELKFNFGEEEFKFPPKDGFVALSKA---PDGYIVKSQHS-----------------------------------------------------------------

6swy1

0.13

0.11

3.97

1.33

EigenThreader

YFLPSRW---QAQPNNSLQLSQDITHLQPNPDYDFAVTWANKSLLTIFYYEIKVLVNSNIVIGYKLVES---INKCQKYGFDLNVFGYCGFDGLITNSTEQSKEYAKPFGRDDVIGCGINFIDGSIFFTKNGIHL--GNAFTDLNDLEFVPYVALRPGNSIKTNFGLNEDFVFDIIGYQDKWKSLAYEHIC------------------RLKFLL---GEDNRFIDLVRPDVNNKGFLKDLQKDAVNESKDVIRHNERQIMKE

4xw3A

0.24

0.15

4.75

3.35

CNFpred

------WQMNPYDRGSAFAIGSDGLCCQSREVEWHGCRATKGLMKGKHYYEVSCHDQGLCRVGWSTMQA------SLDLGTDKFGFGFGGT-GKKSHNK-QFDNYGEEFTMHDTIGCYLDIDKGHVKFSKNGKDLGLAFEIPPHKNQALFPACVLK-NAELKFNFGEEEFKFPPKDGFVALSKA-------------------------------------------------------------------------------

4xw3A

0.23

0.15

4.78

1.00

DEthreader

----NKWQMNPYDRGSAFAIGSDGLCCQSREVEWHGCRATKGLMKGKHYYEVSCHDQGLCRVGWSTMQASL------DLGTDKFGFGFGG-TGKKSHNKQFDNY-GEEFTMHDTIGCYLDIDKGHVKFSKNGKDLGL-AFEIPMKNQALFPACVLKN-AELKFNFGEEEFKFPPKDGFVALSKADIK---SGNA---------------------------------------------------------------------

(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	0.723

(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	6chgB	0.67	2.71	0.204	0.745	model1_6chgB.pdb.gz
2	6pwvD	0.66	2.62	0.218	0.730	model1_6pwvD.pdb.gz
3	4xw3A	0.66	2.11	0.214	0.707	model1_4xw3A.pdb.gz
4	3tojA	0.65	1.73	0.240	0.681	model1_3tojA.pdb.gz
5	6venO	0.64	2.77	0.184	0.722	model1_6venO.pdb.gz
6	6bx3K	0.62	2.84	0.133	0.715	model1_6bx3K.pdb.gz
7	5ji7A	0.60	1.98	0.208	0.650	model1_5ji7A.pdb.gz
8	7b2sA	0.58	2.41	0.222	0.631	model1_7b2sA.pdb.gz
9	7ccbA	0.58	1.69	0.173	0.616	model1_7ccbA.pdb.gz
10	4m00A	0.57	4.43	0.070	0.783	model1_4m00A.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	0.93	catalytic activity
GO:0016740	0.78	transferase activity
GO:1901363	0.74	heterocyclic compound binding
GO:0097159	0.74	organic cyclic compound binding
GO:0003676	0.65	nucleic acid binding
GO:0000166	0.63	nucleotide binding
GO:0046872	0.62	metal ion binding
GO:0035639	0.62	purine ribonucleoside triphosphate binding
GO:0032559	0.62	adenyl ribonucleotide binding
GO:0032550	0.62	purine ribonucleoside binding
GO:0016787	0.61	hydrolase activity
GO:0016887	0.59	ATPase activity
GO:0070035	0.58	purine NTP-dependent helicase activity
GO:0042623	0.58	ATPase activity, coupled
GO:0008186	0.57	RNA-dependent ATPase activity
GO:0042802	0.56	identical protein binding
GO:0022892	0.56	substrate-specific transporter activity
GO:0004872	0.56	receptor activity
GO:0003723	0.56	RNA binding
GO:0015278	0.55	calcium-release channel activity
GO:0000989	0.55	transcription factor activity, transcription factor binding
GO:0070717	0.54	poly-purine tract binding
GO:0016788	0.54	hydrolase activity, acting on ester bonds
GO:0005219	0.54	ryanodine-sensitive calcium-release channel activity
GO:0005509	0.53	calcium ion binding
GO:0005516	0.52	calmodulin binding
GO:0004842	0.51	ubiquitin-protein transferase 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:0009987	0.95	cellular process
GO:0065007	0.86	biological regulation
GO:0050789	0.85	regulation of biological process
GO:0050794	0.84	regulation of cellular process
GO:0008152	0.84	metabolic process
GO:0071704	0.83	organic substance metabolic process
GO:0044237	0.83	cellular metabolic process
GO:0044238	0.82	primary metabolic process
GO:0044260	0.80	cellular macromolecule metabolic process
GO:0044699	0.76	single-organism process
GO:0016043	0.74	cellular component organization
GO:0006807	0.74	nitrogen compound metabolic process
GO:0006139	0.72	nucleobase-containing compound metabolic process
GO:0044763	0.70	single-organism cellular process
GO:0016070	0.70	RNA metabolic process
GO:0080090	0.68	regulation of primary metabolic process
GO:0060255	0.68	regulation of macromolecule metabolic process
GO:0031323	0.68	regulation of cellular metabolic process
GO:0010468	0.66	regulation of gene expression
GO:0006996	0.65	organelle organization
GO:0032268	0.64	regulation of cellular protein metabolic process
GO:0043933	0.63	macromolecular complex subunit organization
GO:0023051	0.63	regulation of signaling
GO:0010646	0.63	regulation of cell communication
GO:0022607	0.62	cellular component assembly
GO:0050896	0.61	response to stimulus
GO:0051171	0.59	regulation of nitrogen compound metabolic process
GO:0031326	0.59	regulation of cellular biosynthetic process
GO:2000112	0.58	regulation of cellular macromolecule biosynthetic process
GO:0051716	0.58	cellular response to stimulus
GO:0006950	0.58	response to stress
GO:0042221	0.57	response to chemical
GO:0019538	0.57	protein metabolic process
GO:0033554	0.56	cellular response to stress
GO:0014070	0.56	response to organic cyclic compound
GO:1901698	0.55	response to nitrogen compound
GO:0070887	0.55	cellular response to chemical stimulus
GO:0065003	0.55	macromolecular complex assembly
GO:0048518	0.55	positive regulation of biological process
GO:0009719	0.55	response to endogenous stimulus
GO:0006974	0.55	cellular response to DNA damage stimulus
GO:0006396	0.55	RNA processing
GO:0071417	0.54	cellular response to organonitrogen compound
GO:0071407	0.54	cellular response to organic cyclic compound
GO:0051336	0.54	regulation of hydrolase activity
GO:0032392	0.54	DNA geometric change
GO:0014074	0.54	response to purine-containing compound
GO:0009605	0.54	response to external stimulus
GO:0008033	0.54	tRNA processing
GO:0006464	0.54	cellular protein modification process
GO:0006417	0.54	regulation of translation
GO:0006281	0.54	DNA repair
GO:0000394	0.54	RNA splicing, via endonucleolytic cleavage and ligation
GO:0071313	0.53	cellular response to caffeine
GO:0051707	0.53	response to other organism
GO:0051179	0.53	localization
GO:0043331	0.53	response to dsRNA
GO:0022618	0.53	ribonucleoprotein complex assembly
GO:0016032	0.53	viral process
GO:0000398	0.53	mRNA splicing, via spliceosome
GO:0048522	0.52	positive regulation of cellular process
GO:0032502	0.52	developmental process
GO:0007165	0.52	signal transduction
GO:0006413	0.52	translational initiation
GO:0051234	0.50	establishment of localization
GO:0044767	0.50	single-organism developmental process

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:0043226	0.85	organelle
GO:0043229	0.84	intracellular organelle
GO:0044444	0.81	cytoplasmic part
GO:0043227	0.81	membrane-bounded organelle
GO:0005737	0.80	cytoplasm
GO:0044422	0.79	organelle part
GO:0043231	0.79	intracellular membrane-bounded organelle
GO:0044446	0.78	intracellular organelle part
GO:0016020	0.65	membrane
GO:0005634	0.64	nucleus
GO:0032991	0.59	macromolecular complex
GO:0043234	0.56	protein complex

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	2agsA	0.454	4.11	0.075	0.605	3.2.1.18	NA
2	0.060	2uwaA	0.471	3.81	0.043	0.597	3.2.1.4	NA
3	0.060	1gpiA	0.485	4.00	0.096	0.639	3.2.1.91	NA
4	0.060	1kitA	0.440	4.36	0.029	0.597	3.2.1.18	NA
5	0.060	2ifwA	0.404	4.12	0.060	0.540	3.4.23.32	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	0.02	2v240	0.562	2.28	0.143	0.624	0.60	III	complex1.pdb.gz	56,57,58,59,156,157
2	0.02	2iwg2	0.520	2.79	0.127	0.593	0.66	III	complex2.pdb.gz	61,89,91,157,158
3	0.02	1ciwC	0.509	3.46	0.070	0.635	0.73	UUU	complex3.pdb.gz	59,62,79,80,89,155
4	0.01	1lu1A	0.510	3.88	0.060	0.662	0.95	ADE	complex4.pdb.gz	60,61,62,88,90,93
5	0.01	2gmpA	0.502	3.48	0.065	0.631	0.64	UUU	complex5.pdb.gz	59,60,78,156,157

	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.