D-I-TASSER Q96KS9-D1

D-I-TASSER results for Q96KS9-D1

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

Input Sequence in FASTA format

>Q96KS9 (214 residues)
MSVPQIHVEEVGAEEGAGAAAPPDDHLRSLKALTEKLRLETRRPSYLEWQARLEEHTWPF
PRPAAEPQASLEEGERGGQEPLLPLREAGQHPPSARSASQGARPLSTGKLEGFQSIDEAI
AWLRKELTEMRLQDQQLARQLMRLRGDINKLKIEHTCRLHRRMLNDATYELEERDELADL
FCDSPLASSFSLSTPLKLIGVTKMNINSRRFSLC

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSVPQIHVEEVGAEEGAGAAAPPDDHLRSLKALTEKLRLETRRPSYLEWQARLEEHTWPFPRPAAEPQASLEEGERGGQEPLLPLREAGQHPPSARSASQGARPLSTGKLEGFQSIDEAIAWLRKELTEMRLQDQQLARQLMRLRGDINKLKIEHTCRLHRRMLNDATYELEERDELADLFCDSPLASSFSLSTPLKLIGVTKMNINSRRFSLC
Prediction	CCCCCSSSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCCCCCCHHHHHCCSSSCCCCCCSSCC
Confidence	9988525664256667777889725789999999998211158418999999996357888775442221110013564333343332357763335556888888531124242999999999999999999999999999999999999999999999999988777653030454020458887655543225552500211344310039
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSVPQIHVEEVGAEEGAGAAAPPDDHLRSLKALTEKLRLETRRPSYLEWQARLEEHTWPFPRPAAEPQASLEEGERGGQEPLLPLREAGQHPPSARSASQGARPLSTGKLEGFQSIDEAIAWLRKELTEMRLQDQQLARQLMRLRGDINKLKIEHTCRLHRRMLNDATYELEERDELADLFCDSPLASSFSLSTPLKLIGVTKMNINSRRFSLC
Prediction	7744514155135746566544466304404200541514244322340343047440644445546555455566444543244454463544454455565445464344174054004202520451344145004302503530450325510540462065143415636524412151435452323310331212323153442437
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCSSSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCCCCCCHHHHHCCSSSCCCCCCSSCC
MSVPQIHVEEVGAEEGAGAAAPPDDHLRSLKALTEKLRLETRRPSYLEWQARLEEHTWPFPRPAAEPQASLEEGERGGQEPLLPLREAGQHPPSARSASQGARPLSTGKLEGFQSIDEAIAWLRKELTEMRLQDQQLARQLMRLRGDINKLKIEHTCRLHRRMLNDATYELEERDELADLFCDSPLASSFSLSTPLKLIGVTKMNINSRRFSLC

1vt4I3

0.06

2.51

0.56

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

2tmaA

0.08

0.07

3.00

0.68

EigenThreader

QMLK-----LDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEEIKTVTNNLKSLEAQAEKYSQK

6vq6H

0.14

0.10

3.52

0.62

FFAS-3D

---------------DRIEIFPSRMAQTIMKARLKGAQLKKKSDALTLMGEVMREAAFSLAEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTYHEGTDSYELTGLARGGEQLAKLKRNYAKELASLQTSFVTLDEAIKITNRRVNAIRIERTLAYIITELDE-----REREEFYRL----------------------------------

6w2wA

0.15

0.14

4.71

0.74

SPARKS-K

--SEEVNERVKQLAEKAKEATDKEEVIEIVKELAELAKQSTDPNVVAEIVYQLAEVAEHSTDPEQEALRLAEEQGDEELAEAARLALKEEARQLLSKDPE------------NEAAKECLKAVRAALEAALLALLLLAKQLATAALRAVEAACQLAKQIAKKCIKAASEAAEEASKAAEEAQRHPDSQ--KARDEIKEASQKAEEVKERCERA-

3r6nA

0.16

0.08

2.81

0.55

CNFpred

------------------------DHLRQLQNIIQATSRE--IMWINDCEEEELLYDWSD-------------------------------KNTNIAQKQE----------AFSIRMSQLEVKEKELNKLKQESDQLVLNQHPASDKIEAYTLQTQWSWILQITKCIDVHLKENAAYFQFFE--------------------------------

6z9lA

0.06

0.04

1.64

0.83

DEthreader

----------------------------------------------------------------------K--KDADQSDQVVQNDALDSQVTQQVDEAKKVDEATAIEKAKEQV--ATDTQAVDEQQKVVDQAQTDVNQQQAVVDEKAKETNAAKVQNEKDQQAVTAAKQEQAKLEELAKNAEAEKVKAEKE--Q----AAKEAELANKQTAT

4q2cA

0.06

2.51

0.84

MapAlign

RELVARRLRDAGLPLFNARAPHGTISANVLETVLADVFGLSGRSARWVAFAVGPTATSNQFGRVTDYLRHRYPEDVVVVNLVHGHSDLSALLQELRQKGEEIFQLQGVYDEALGDEQLGAVVAGQWREVREARTLGRFTLLRSWLALRSLWERTFKAQQKVLREDSLDARVLDPLLDRSSLLRGYRPLVFDASGRAVGRWIVRIDPELGIVVES

5nnvA

0.17

0.16

5.24

0.68

MUSTER

ISAKEAKIEDTRDKIQALDESVDEQVLLVTSEELEKLE-KERKKNAVQNQEQLEEAIVQFQQKETVLKEELSKQEAVFETLQAEVKQLRAQVKEKQQLSNELTELKIAKEQACKGEEDNLARLKKELTETELALKEAKEDLSFLTSTSGEEKLEEAAKHKLNDKTKTIELIALRRDQRIKLQHG-LDTYERELKEKRLY--------KQKTTLL

2yy0B

0.19

0.05

1.51

0.47

HHsearch

---------------------------------------------------------------------------------NSALDFLKHHL-------------GAATP---EN--PEIELLRLELAEMKEKYEAIVEENKKLKAKLAQYE--------------------------------------------------------------

2gkoA

0.04

2.10

0.49

CEthreader

HVAGSALANGGTGSGVYGVAPEADLWAYKVLGDDGSGYADDIAEAIRHAGDQATALNTKVVINMSLGSSGESSLITNAVDYAYDKGVLIIAAIGYPGALVNAVAVAALENTIQNGTYRVADFSSRGHKRTAGDYVIQKGDVEISATSMASPHAAGLAAKIWAQSPAASNVDVRGELQTRASVNDILSGNSAGSGDDIASGFGFAKVQ-------

(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	0.3928

(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	4a01A	0.50	4.72	0.046	0.738	model1_4a01A.pdb.gz
2	6nbqF	0.48	5.43	0.040	0.785	model1_6nbqF.pdb.gz
3	4av3A	0.48	4.78	0.055	0.710	model1_4av3A.pdb.gz
4	6csxB	0.47	5.53	0.039	0.771	model1_6csxB.pdb.gz
5	6s7tA	0.47	5.80	0.042	0.818	model1_6s7tA.pdb.gz
6	6t15a	0.47	5.32	0.026	0.757	model1_6t15a.pdb.gz
7	6u8yX	0.47	5.71	0.058	0.813	model1_6u8yX.pdb.gz
8	5xamA	0.47	5.57	0.070	0.780	model1_5xamA.pdb.gz
9	1ocrN	0.47	5.47	0.052	0.766	model1_1ocrN.pdb.gz
10	5lq3A	0.46	4.99	0.081	0.720	model1_5lq3A.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:1901363	0.60	heterocyclic compound binding
GO:0097159	0.60	organic cyclic compound binding
GO:0003824	0.59	catalytic activity
GO:0046872	0.58	metal ion binding
GO:0046914	0.52	transition metal ion binding
GO:0022891	0.51	substrate-specific transmembrane transporter activity
GO:0046906	0.50	tetrapyrrole binding
GO:0016676	0.50	oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor
GO:0015078	0.50	hydrogen ion transmembrane transporter activity
GO:0015002	0.50	heme-copper terminal oxidase 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	0.69	cellular process
GO:0044699	0.65	single-organism process
GO:0008152	0.62	metabolic process
GO:0071704	0.61	organic substance metabolic process
GO:0044763	0.60	single-organism cellular process
GO:0044238	0.60	primary metabolic process
GO:0044237	0.60	cellular metabolic process
GO:0006807	0.59	nitrogen compound metabolic process
GO:1901360	0.58	organic cyclic compound metabolic process
GO:0034641	0.58	cellular nitrogen compound metabolic process
GO:0006139	0.57	nucleobase-containing compound metabolic process
GO:0044765	0.53	single-organism transport
GO:0044710	0.53	single-organism metabolic process
GO:0019637	0.52	organophosphate metabolic process
GO:0006796	0.52	phosphate-containing compound metabolic process
GO:1901564	0.51	organonitrogen compound metabolic process
GO:1901135	0.51	carbohydrate derivative metabolic process
GO:0055085	0.51	transmembrane transport
GO:0044281	0.51	small molecule metabolic process
GO:0006811	0.51	ion transport
GO:0098662	0.50	inorganic cation transmembrane transport
GO:0046034	0.50	ATP metabolic process
GO:0045333	0.50	cellular respiration
GO:0016310	0.50	phosphorylation
GO:0015992	0.50	proton transport

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:0044425	1.00	membrane part
GO:0016020	1.00	membrane
GO:0005886	0.83	plasma membrane
GO:0044424	0.77	intracellular part
GO:0043226	0.66	organelle
GO:0043229	0.65	intracellular organelle
GO:0043227	0.65	membrane-bounded organelle
GO:0016021	0.62	integral component of membrane
GO:0043231	0.54	intracellular membrane-bounded organelle
GO:0044444	0.51	cytoplasmic part

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	2iukB	0.432	5.84	0.052	0.762	1.13.11.12	NA
2	0.060	2p0mB	0.423	6.00	0.063	0.757	1.13.11.33	39
3	0.060	1s5jA	0.451	5.86	0.077	0.771	2.7.7.7	165,169
4	0.060	1occA	0.464	5.47	0.051	0.771	1.9.3.1	113
5	0.060	3bicA	0.413	5.61	0.020	0.715	5.4.99.2	109

	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	0.06	1m57A	0.449	5.43	0.050	0.743	0.27	PEH	complex1.pdb.gz	119,122,126,201
2	0.05	1ocoN	0.466	5.46	0.041	0.766	0.14	HEA	complex2.pdb.gz	53,108,114,126,130
3	0.04	1v54A	0.466	5.46	0.052	0.766	0.16	HEA	complex3.pdb.gz	122,127,130,131,134,192
4	0.01	1ydiA	0.325	4.82	0.051	0.495	0.22	III	complex4.pdb.gz	46,71,74,75,113,132
5	0.01	3fyeA	0.450	5.49	0.050	0.748	0.19	DMU	complex5.pdb.gz	108,115,116
6	0.01	1oczN	0.467	5.45	0.042	0.762	0.17	HEA	complex6.pdb.gz	122,129,130
7	0.01	2ibfA	0.287	5.15	0.067	0.467	0.23	III	complex7.pdb.gz	119,122,126,130,133,134,137
8	0.01	2gdcA	0.320	5.93	0.094	0.598	0.27	III	complex8.pdb.gz	67,74,77,81,125,126,129
9	0.01	1zw2A	0.284	4.81	0.040	0.421	0.23	III	complex9.pdb.gz	52,56,115,119,194,198,201
10	0.01	2ibfA	0.287	5.15	0.067	0.467	0.27	III	complex10.pdb.gz	117,120,121,124,127,128

	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.