D-I-TASSER Q8TDR2-D2

D-I-TASSER results for Q8TDR2-D2

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

Input Sequence in FASTA format

>Q8TDR2 (131 residues)
ARRRPEGGGGSARPRYSLLAEIGRGSYGVVYEAVAGRSGARVAVKKIRCDAPENVELALA
EFWALTSLKRRHQNVVQFEECVLQRNGLAQRMSHGNKSSQLYLRLVETSLKGERILGYAE
EPCYLWFVMEF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| ARRRPEGGGGSARPRYSLLAEIGRGSYGVVYEAVAGRSGARVAVKKIRCDAPENVELALAEFWALTSLKRRHQNVVQFEECVLQRNGLAQRMSHGNKSSQLYLRLVETSLKGERILGYAEEPCYLWFVMEF
Prediction	CCCCCCCCCCCCCCCSSSSCSSCCCCCSSSSSSSSCCCCCSSSSSSSSCCCCCCHHHHHHHHHHHHHHHHCCCCSCSSSSSSSSCCSSSSSSSCCCCCHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHCC
Confidence	98788888987421111201333655669999998899969999999658988989999999999997207996515888998599689998547986899998569999967742312548999998739
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| ARRRPEGGGGSARPRYSLLAEIGRGSYGVVYEAVAGRSGARVAVKKIRCDAPENVELALAEFWALTSLKRRHQNVVQFEECVLQRNGLAQRMSHGNKSSQLYLRLVETSLKGERILGYAEEPCYLWFVMEF
Prediction	85544675545425405315413621203012032364542000220315477414201400420340475151004033003556401000133443023004306451546403624432210122255
	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 AttentionPotential. 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

CCCCCCCCCCCCCCCSSSSCSSCCCCCSSSSSSSSCCCCCSSSSSSSSCCCCCCHHHHHHHHHHHHHHHHCCCCSCSSSSSSSSCCSSSSSSSCCCCCHHHHHHHCCCCCCHHHHCCCHHHHHHHHHHHCC
ARRRPEGGGGSARPRYSLLAEIGRGSYGVVYEAVAGRSGARVAVKKIRCDAPENVELALAEFWALTSLKRRHQNVVQFEECVLQRNGLAQRMSHGNKSSQLYLRLVETSLKGERILGYAEEPCYLWFVMEF

1z57A

0.18

0.16

5.21

1.17

DEthreader

SMHLICDV---LSARYEIVDTLGEGAFGKVVECIDHKGGRHVAVKIVKN-VDRYCEAARSEIQVLEHLNTTDSRCVQMLEWFEHHGHICIVFELLGL--ST--F-----IRKAYQICVNLTHKVVDFGS--

4oliA1

0.14

0.13

4.44

1.56

SPARKS-K

-----LSFHRVDQKEITQLSHLGQGTRTNVYEGRLR-VELRVVLKVLDPSHHDIALAFYETASLMSQV--SHTHLAFVHGVCVRGPENIMVTEYVEHGP-LDVWLVPMAWKMVVAQQLASALSYLENKNLV

1q99B

0.15

4.89

0.47

MapAlign

-GYHPAFKGEPYKARYILVRKLGWGHFSTVWLAKDMVNNTHVAMKIVRG-DKVYTEAAEDEIKLLQRVNDDSMGALKLLDHFNHGVHVVMVFEVLGENLLALIKKYEHRGIPLIYVKQISKQLLLGLDY--

1q99B

0.14

0.13

4.46

0.28

CEthreader

GYHPAFKGEPYKDARYILVRKLGWGHFSTVWLAKDMVNNTHVAMKIVR-GDKVYTEAAEDEIKLLQRVNDAANHILKLLDHFNHKVHVVMVFEVLGENLLALIKKYEHR-----GIPLIYVKQISKQLLLG

3p1aA

0.20

6.35

1.20

MUSTER

PGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPGPKDRARKLAEVGSHEKVG-QHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHS

6ygnA

0.16

5.31

0.67

HHsearch

TREMTKASHSSTYEKYMIAEDLGRGEFGIVHRCVETSSKKTYMAKFVKVKG-TDQVLVKKEISILNIA--RHRNILHLHESFESMEELVMIFEFISGLDRINTSELNEREIVSYVHQVCEALQFLHSHNDI

4aguA

0.22

0.19

6.01

1.39

FFAS-3D

-------------EKYEKIGKIGEGSYGVVFKCRNRDTGQIVAIKKFLESEDPVKKIALREIRMLKQL--KHPNLVNLLEVFRRKRRLHLVFEYCDHTVLHELDRYQRGVPKSITWQTLQAVNFCHK----

4qnyA1

0.19

6.14

0.62

EigenThreader

SLAELQAEVCRLDDRYLLERIIGAGSYGVVIRARDTKSDNRVAMKRVNFEEVILAKRILREIKLLAHFN--DDNIIGLRNILTPFDHFYIVMDIMETDLKQVLRSGQELTEAHIQFFIYQALRALHIIHSA

1koaA

0.18

0.15

4.99

1.69

CNFpred

--------------HYDIHEELGTGAFGVVHRVTERATGNNFAAKFVMTPHESDKETVRKEIQTMSVL--RHPTLVNLHDAFEDDNEMVMIYE-GELFEKVADEKMSEDEAVEYMRQVCKGLCHMHENNYV

1ql6A

0.17

0.15

5.00

1.17

DEthreader

------STH-GFYENYEPKEILGRGVSSVVRRCIHKPTCKEYAVKIIDVTVQELREATLKEVDILRKVSG-HPNIIQLKDTYETNTFFFLVFDLMKK-GEL-DY-----ETRKIMALLVILHDLNLTDFG-

(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	0.7448

(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 AttentionPotential, 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	3kvwA	0.77	2.74	0.213	0.939	model1_3kvwA.pdb.gz
2	1z57A	0.77	2.99	0.189	0.939	model1_1z57A.pdb.gz
3	2vx3A	0.76	3.01	0.197	0.939	model1_2vx3A.pdb.gz
4	1q99B	0.76	2.99	0.151	0.931	model1_1q99B.pdb.gz
5	2wu6A	0.75	2.96	0.165	0.931	model1_2wu6A.pdb.gz
6	1wakA	0.75	2.80	0.175	0.939	model1_1wakA.pdb.gz
7	4ianA	0.74	2.85	0.179	0.908	model1_4ianA.pdb.gz
8	4btjA	0.74	2.75	0.179	0.908	model1_4btjA.pdb.gz
9	3lltA	0.74	3.12	0.157	0.939	model1_3lltA.pdb.gz
10	3ll6A	0.73	3.06	0.164	0.931	model1_3ll6A.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:0016301	0.99	kinase activity
GO:0004672	0.98	protein kinase activity
GO:0004674	0.96	protein serine/threonine kinase activity
GO:1901363	0.82	heterocyclic compound binding
GO:0097159	0.82	organic cyclic compound binding
GO:0032555	0.81	purine ribonucleotide binding
GO:0032550	0.81	purine ribonucleoside binding
GO:0005524	0.80	ATP 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	0.96	cellular process
GO:0065007	0.87	biological regulation
GO:0050789	0.87	regulation of biological process
GO:0050794	0.86	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:0043170	0.82	macromolecule metabolic process
GO:0044260	0.81	cellular macromolecule metabolic process
GO:0019538	0.80	protein metabolic process
GO:0006468	0.79	protein phosphorylation
GO:0044699	0.75	single-organism process
GO:0044763	0.69	single-organism cellular process
GO:0007165	0.62	signal transduction
GO:0050896	0.61	response to stimulus
GO:0016043	0.60	cellular component organization
GO:0048518	0.59	positive regulation of biological process
GO:0048519	0.57	negative regulation of biological process
GO:0006810	0.56	transport
GO:0048523	0.55	negative regulation of cellular process
GO:0051128	0.54	regulation of cellular component organization
GO:0050793	0.53	regulation of developmental process
GO:0065008	0.52	regulation of biological quality
GO:0051239	0.52	regulation of multicellular organismal process
GO:0008104	0.51	protein localization
GO:0007049	0.51	cell cycle
GO:2000026	0.50	regulation of multicellular organismal development
GO:0045184	0.50	establishment of protein localization
GO:0042221	0.50	response to chemical
GO:0035556	0.50	intracellular signal transduction
GO:0032879	0.50	regulation of localization
GO:0022607	0.50	cellular component 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:0044424	1.00	intracellular part
GO:0043229	0.79	intracellular organelle
GO:0005737	0.77	cytoplasm
GO:0043227	0.71	membrane-bounded organelle
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0005634	0.60	nucleus
GO:0044444	0.59	cytoplasmic part
GO:0016020	0.53	membrane
GO:0044422	0.52	organelle 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	2np8A	0.686	3.07	0.160	0.878	2.7.11.1	NA
2	0.060	1cmkE	0.689	2.95	0.142	0.870	2.7.11.11 2.7.1.37	NA
3	0.060	1zrzA	0.685	3.04	0.161	0.878	2.7.11.13	50,54
4	0.060	3lm0A	0.689	2.97	0.159	0.870	2.7.11.1	47
5	0.060	2biyA	0.685	2.94	0.139	0.863	2.7.11.1	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	0.44	2vx3B	0.756	2.88	0.198	0.931	1.06	D15	complex1.pdb.gz	22,23,24,25,27,28,29,30,43,45,92,93,95,96,126
2	0.41	3begA	0.740	2.84	0.179	0.916	1.04	ANP	complex2.pdb.gz	22,25,26,27,28,30,93,95
3	0.29	2gnlA	0.699	2.98	0.156	0.878	0.81	H52	complex3.pdb.gz	22,23,24,30,43,93,95,125
4	0.28	3fc2A	0.719	3.09	0.177	0.924	0.90	IBI	complex4.pdb.gz	20,21,22,30,32,76,92,93,95,96,98
5	0.24	3anqA	0.745	3.03	0.197	0.931	0.84	EHB	complex5.pdb.gz	27,30,43,45,92,93,95
6	0.20	3dbcA	0.714	3.07	0.154	0.916	0.87	2FR	complex6.pdb.gz	22,24,25,30,43,76,92,93,95,98
7	0.19	1xh5A	0.691	2.97	0.148	0.870	0.98	BU3	complex7.pdb.gz	27,28,29,87
8	0.18	3l9lA	0.696	2.97	0.148	0.870	0.81	L9L	complex8.pdb.gz	22,26,30,43,45,92,93,94,95,125,126
9	0.17	3db6A	0.702	3.09	0.138	0.916	0.84	FRS	complex9.pdb.gz	22,23,30,43,45,58,61,62,65,76,78,90,92,93,95,125
10	0.06	3dneA	0.698	2.93	0.150	0.870	0.89	LL1	complex10.pdb.gz	22,23,30,43,92,93,94,95,126

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.