D-I-TASSER Q96A26-D1

D-I-TASSER results for Q96A26-D1

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

Input Sequence in FASTA format

>Q96A26 (154 residues)
MGSLSGLRLAAGSCFRLCERDVSSSLRLTRSSDLKRINGFCTKPQESPGAPSRTYNRVPL
HKPTDWQKKILIWSGRFKKEDEIPETVSLEMLDAAKNKMRVKISYLMIALTVVGCIFMVI
EGKKAAQRHETLTSLNLEKKARLKEEAAMKAKTE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGSLSGLRLAAGSCFRLCERDVSSSLRLTRSSDLKRINGFCTKPQESPGAPSRTYNRVPLHKPTDWQKKILIWSGRFKKEDEIPETVSLEMLDAAKNKMRVKISYLMIALTVVGCIFMVIEGKKAAQRHETLTSLNLEKKARLKEEAAMKAKTE
Prediction	CCCHHHHHHHCCCSSSHHHCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHSSSSSCCCCCHHHCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence	9741344553052121111354034443136676543776678988999996201468887898034311344346788443935169999998511344678899999999999999999788888188688998999999989999874129
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGSLSGLRLAAGSCFRLCERDVSSSLRLTRSSDLKRINGFCTKPQESPGAPSRTYNRVPLHKPTDWQKKILIWSGRFKKEDEIPETVSLEMLDAAKNKMRVKISYLMIALTVVGCIFMVIEGKKAAQRHETLTSLNLEKKARLKEEAAMKAKTE
Prediction	7331411322033002015642343133345442453453225566447445544541453424623320000044145475127403440053044312020022013313321320012034137445413543362154246635465668
	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                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHCCCSSSHHHCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHSSSSSCCCCCHHHCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCC
MGSLSGLRLAAGSCFRLCERDVSSSLRLTRSSDLKRINGFCTKPQESPGAPSRTYNRVPLHKPTDWQKKILIWSGRFKKEDEIPETVSLEMLDAAKNKMRVKISYLMIALTVVGCIFMVIEGKKAAQRHETLTSLNLEKKARLKEEAAMKAKTE

5hk1A

0.08

3.28

0.46

CEthreader

QYAGLDHELAFSRLIVELRRLHPGHVLPDEELQWVFVNAMCLLHASLSEYVLGRYWAEISDTIISGTFHQWREGTTKSEVFYPGETVVHGPGEATAVEWGPNTWMVEYGRGVIPSTLAFALADTVFSTQDFLTLFYTLRSYARGLRLELTTYLF

7d58A

0.07

2.93

0.70

EigenThreader

TMKLTEIIFLNDVIKKHRISGAKTQMIMEDWDFLQLQCALYINSELTKANLVTPRNGEPLIAAIQDFLTGAYLLTLSMDKGTLGSGSMSRLARLAPVYLSNRGLKAKYELLNAGYKKCDEYIEALNTGKLQQTLEALISACLRPLTMALCGSKG

7blnA6

0.10

0.08

2.88

0.54

FFAS-3D

IVSQDQVDSIMNLVSTLI--------------------------QDQPDQPVEDPDPEDFADEQSLVGRFIHLLRSEDPDQQ------YLILNTARKHFRIRFTLPPL---VFAAYQLAFRYKENSKVDDKWEKKCQKIFSFAHQTISALIKAE

5cwjA

0.13

0.11

3.84

0.79

SPARKS-K

SGTEESLRQAIEDVAQLAKSQDSEVLEEAIRVILRIAKESGS-----------------EEALRQAIRAVAEIAKEAQDSEVLEERVILRIAKESGSEEALRQAIRAVAEIAKEAEEAIRVIRQIAEESGS--EEARRQAERAEEEIRRRAQ--

4u96A

0.12

0.09

3.18

0.54

CNFpred

KISIHEVVKTLVEAIILVFLVMYLFLQNFR--------------------------------ATLIPTIAVPVVL----------LGTFAVLAFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEGLPPKEATRKSMGQIQGALVGIAMVL

3javA

0.03

0.02

1.27

0.83

DEthreader

DTKLIIC-IKHTKQLLLDIMNASRFRMKVAQQEE-LQFDGESNIDYNMKELEVIKYPYATAEFLWKKLRAQPVLY----------------------WC--ARNMSFWSSISFNLAVLMNLLVAFFYP-------------SHGLRSGGGVGDL

1eqrA

0.09

3.45

0.66

MapAlign

QVREVMEALVRHLWLEAERRYGSDKPDLRNPMELTDVADLLKSVEFAVFAGPANDPKGRVAALIDEYGNFVKIYGAKGLDGDMIFFGAKKIVADAMGALRLKVGKDEVGGGSVRIHNGDMQQTVFGILGINEEEQREKFGFLLDARLTMLLTGT

1lihA

0.13

0.12

4.30

0.59

MUSTER

MGLFSSLQHCQQGFVISNERQQQSELTSTWDLMLQTRINLSRSAARMMMDASNQQSSAKTDLLQNAKTTLAQAAAHYANFKNMTPL-----PAMAEASANVDEKYQRYQAALAELIQFLDNGMDAYFAQPTMQNALGEALGNYARVSENLYRQT

1vt4I3

0.15

0.12

4.16

0.86

HHsearch

-----EYAL-----HRSIVDH-YNIPKTFDSDDL--------IPPYLD---QYFYSLKNIEHPERMTLFRMVFLFRFLEQKIRHDNSILNTLQQL----KFYKPYICKYERLVNAILDFL-PKIEENLISKYTDLLIALMAEDEAIHKQVQRGG

4twkA

0.05

2.40

0.43

CEthreader

ALEQPHEISQRTTIVIQKQTFISQHSCVNSTELDELIQQIVAAINAGIIPLGNTSNQISHWDLGSSFFFAGTVITTIGFGNISPRTFCIIYALLGIPLFGFLLAGVGDQLGTIFGKGIAKVEDTFIKWNVSQTKIRIISTIIFILFGCVLFVAL

(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	0.4912

(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	6a70B	0.56	4.44	0.063	0.857	model1_6a70B.pdb.gz
2	5k47A	0.53	4.62	0.072	0.844	model1_5k47A.pdb.gz
3	6at7B	0.53	4.14	0.047	0.766	model1_6at7B.pdb.gz
4	6e59A	0.52	4.75	0.077	0.851	model1_6e59A.pdb.gz
5	4a01A	0.51	4.31	0.083	0.779	model1_4a01A.pdb.gz
6	2zqpY	0.51	4.00	0.074	0.766	model1_2zqpY.pdb.gz
7	5lpnB	0.51	3.67	0.096	0.714	model1_5lpnB.pdb.gz
8	2inrA	0.51	4.02	0.037	0.734	model1_2inrA.pdb.gz
9	6u7hA	0.51	4.77	0.047	0.838	model1_6u7hA.pdb.gz
10	6qd6A1	0.51	4.56	0.043	0.838	model1_6qd6A1.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	0.69	heterocyclic compound binding
GO:0097159	0.69	organic cyclic compound binding
GO:0003824	0.65	catalytic activity
GO:0003676	0.65	nucleic acid binding
GO:0035639	0.60	purine ribonucleoside triphosphate binding
GO:0032555	0.60	purine ribonucleotide binding
GO:0032550	0.60	purine ribonucleoside binding
GO:0016787	0.60	hydrolase activity
GO:0032559	0.58	adenyl ribonucleotide binding
GO:0016462	0.58	pyrophosphatase activity
GO:0061505	0.57	DNA topoisomerase II activity
GO:0008094	0.57	DNA-dependent ATPase 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	0.97	cellular process
GO:0048518	0.96	positive regulation of biological process
GO:0009966	0.96	regulation of signal transduction
GO:0090200	0.95	positive regulation of release of cytochrome c from mitochondria
GO:0071456	0.95	cellular response to hypoxia
GO:0006919	0.95	activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0044699	0.56	single-organism 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:0005739	1.00	mitochondrion
GO:0005737	1.00	cytoplasm
GO:0044421	0.54	extracellular region part
GO:0070062	0.53	extracellular exosome

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	1mhsA	0.497	5.27	0.067	0.883	3.6.3.6	NA
2	0.060	2iukA	0.465	4.85	0.080	0.812	1.13.11.12	NA
3	0.060	1v4tA	0.484	3.64	0.042	0.656	2.7.1.2 2.7.1.1	NA
4	0.060	3crlB	0.470	4.05	0.028	0.695	2.7.11.2	137
5	0.060	2occN	0.471	5.11	0.036	0.792	1.9.3.1	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	0.01	3d9dC	0.507	4.91	0.080	0.870	0.52	N6C	complex1.pdb.gz	114,117,121,135
2	0.01	3d9eD	0.511	4.92	0.099	0.851	0.42	N8C	complex2.pdb.gz	116,119,122,123,126
3	0.01	3foeA	0.510	4.03	0.060	0.734	0.73	QNA	complex3.pdb.gz	116,118,122,135
4	0.01	3d9eC	0.507	4.94	0.073	0.864	0.49	N8C	complex4.pdb.gz	115,118,121,122,136
5	0.01	3fofA	0.511	4.13	0.060	0.747	0.52	QNA	complex5.pdb.gz	125,131,142
6	0.01	3o01B	0.493	4.73	0.063	0.786	0.51	DXC	complex6.pdb.gz	112,115,119
7	0.01	3fofB	0.465	4.44	0.044	0.734	0.50	QNA	complex7.pdb.gz	131,139,142

	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.