D-I-TASSER Q9BZF9-D3

D-I-TASSER results for Q9BZF9-D3

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

Input Sequence in FASTA format

>Q9BZF9 (127 residues)
QNEMIVEEFKRDEGKLIEENKRLQKELSMCEMEREKKGRKVTEMEGQAKELSAKLALSIP
AEKFENMKSSLSNEVNEKAKKLVEMELTIEMKNHYVPLKVSEDMKKSHDAIIDDLNRKLL
DVTQKYT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| QNEMIVEEFKRDEGKLIEENKRLQKELSMCEMEREKKGRKVTEMEGQAKELSAKLALSIPAEKFENMKSSLSNEVNEKAKKLVEMELTIEMKNHYVPLKVSEDMKKSHDAIIDDLNRKLLDVTQKYT
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	8188999999879999999999999999999999998829999999999999999940768899999999999999999999999999999932444778899999999988999999999866039
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| QNEMIVEEFKRDEGKLIEENKRLQKELSMCEMEREKKGRKVTEMEGQAKELSAKLALSIPAEKFENMKSSLSNEVNEKAKKLVEMELTIEMKNHYVPLKVSEDMKKSHDAIIDDLNRKLLDVTQKYT
Prediction	8555225504544552365354146415414353554654245145415624441445245642551454046425644442352525253555435264366146525544651454157336628
	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

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
QNEMIVEEFKRDEGKLIEENKRLQKELSMCEMEREKKGRKVTEMEGQAKELSAKLALSIPAEKFENMKSSLSNEVNEKAKKLVEMELTIEMKNHYVPLKVSEDMKKSHDAIIDDLNRKLLDVTQKYT

3na7A1

0.09

0.08

3.02

1.13

FFAS-3D

--RKDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKMSEIKSERELRSLNIEEDIAKERSNQANREIENLQNE------IKRKSEKQEDLKKEMLELEKLALEL-----

6jlbA

0.06

2.49

1.33

DEthreader

DRVRSLETENAGLRLRITESEEVVSREVSGIKAAYEAELGDARKTLDSVAKERARLQLELSKVREEFKELKARNTKKEGDLIAAQARLKDLEALLSKEAALSTALSEKRTLEGELHDLRGQVAKLEA

2tmaA1

0.13

0.12

4.11

0.34

CEthreader

QLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQ----LVEEELDRAQERLATALQKLEEAEKAADESERG----MKVIESRAQKDEEKMEIQEIQLKEAKHI--

2tmaA

0.11

3.98

0.45

EigenThreader

EKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEEIKTVTNNLKSLEAQAEKYSQVLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYKAISEELD

2tmaA1

0.15

0.14

4.79

1.12

FFAS-3D

--EADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEDVASLNRRIQLVEEELDRAQERLATALQKLEEAEK--AADESERGMKVIESRAQKDEEKMEIQEIQL-

4tqlA1

0.14

4.82

0.87

SPARKS-K

ARDRMEKLYKEMVELIQKAIELMRKIFQEVKQEVEKAIELLEKLKQIMQEAKQKMEKLLLKEEMKKMKEKMEKLLKEMKQRMEEVKKLEKIKKN-IDKKIAEDLIKKAEENIKEAKKIAEQLVKRAK

2tmaA

0.16

5.24

0.71

CNFpred

IQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEEIKTVNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAET--RAEFAERSVTKLEKSIDDLEDELYAQKLKYK

7kogB

0.14

4.82

1.33

DEthreader

RIHEIEKQKKRLEVEKDELQAALEEAEAALEQEENKVLRSQLELSQVRQEIDRRIQ-EKEEEFENTRKNHQRALDSMQASLEAEAKGKAEALMKKKLEADINELEIALDHANKANSEAQKTIKKYQQ

7nmqA

0.04

2.06

0.47

MapAlign

LSRINANYWLDTAKPQIQKTARNIVNYDEQFQNYYDTLVETVQKAGLKEGINDLITTINTNSKEVTDVIKMLQDFKGKLYQNSTDFKNNVGGPDGKGGLTAILAGQIPQLQAEIEQLRSTQKKHFDD

3na7A1

0.17

5.41

0.91

MUSTER

-LEPLIREKRKDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASI--QKKMSEIKS--ERELRSLNIEEDIAKERSNQANR--EIENLQNEIKRKSEKQEDLKKEMLELEKLAL

(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	0.5208

(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	6ewyA	0.81	2.34	0.104	0.984	model1_6ewyA.pdb.gz
2	6vq6H	0.79	2.58	0.096	0.976	model1_6vq6H.pdb.gz
3	3hhmB	0.79	2.38	0.066	0.953	model1_3hhmB.pdb.gz
4	5nnvA	0.79	2.37	0.089	0.976	model1_5nnvA.pdb.gz
5	3na7A	0.78	2.68	0.072	0.976	model1_3na7A.pdb.gz
6	6z9lA	0.78	2.64	0.080	0.984	model1_6z9lA.pdb.gz
7	6yvuB	0.78	2.53	0.072	0.984	model1_6yvuB.pdb.gz
8	3sogA	0.78	2.28	0.076	0.929	model1_3sogA.pdb.gz
9	6z6fD	0.78	2.54	0.120	0.984	model1_6z6fD.pdb.gz
10	6x80A	0.78	2.71	0.049	0.961	model1_6x80A.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	0.53	catalytic 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	0.87	cellular process
GO:0065007	0.82	biological regulation
GO:0050794	0.81	regulation of cellular process
GO:0048583	0.76	regulation of response to stimulus
GO:0023051	0.76	regulation of signaling
GO:0009966	0.75	regulation of signal transduction
GO:0048518	0.74	positive regulation of biological process
GO:0080090	0.73	regulation of primary metabolic process
GO:0060255	0.73	regulation of macromolecule metabolic process
GO:0048522	0.73	positive regulation of cellular process
GO:0031323	0.73	regulation of cellular metabolic process
GO:1902531	0.72	regulation of intracellular signal transduction
GO:0048523	0.72	negative regulation of cellular process
GO:0050790	0.71	regulation of catalytic activity
GO:0031325	0.71	positive regulation of cellular metabolic process
GO:0010604	0.71	positive regulation of macromolecule metabolic process
GO:0050896	0.68	response to stimulus
GO:0032879	0.67	regulation of localization
GO:0006950	0.67	response to stress
GO:0080134	0.66	regulation of response to stress
GO:0032386	0.66	regulation of intracellular transport
GO:0007165	0.66	signal transduction
GO:0042990	0.65	regulation of transcription factor import into nucleus
GO:0042307	0.65	positive regulation of protein import into nucleus
GO:0033554	0.64	cellular response to stress
GO:0042981	0.63	regulation of apoptotic process
GO:0035556	0.63	intracellular signal transduction
GO:0009968	0.62	negative regulation of signal transduction
GO:0009411	0.62	response to UV
GO:0008630	0.62	intrinsic apoptotic signaling pathway in response to DNA damage
GO:0032268	0.60	regulation of cellular protein metabolic process
GO:0043085	0.59	positive regulation of catalytic activity
GO:0032270	0.59	positive regulation of cellular protein metabolic process
GO:1902532	0.58	negative regulation of intracellular signal transduction
GO:0051336	0.53	regulation of hydrolase activity
GO:0043122	0.53	regulation of I-kappaB kinase/NF-kappaB signaling
GO:0032101	0.53	regulation of response to external stimulus
GO:0031347	0.53	regulation of defense response
GO:0050728	0.52	negative regulation of inflammatory response
GO:0043280	0.52	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0042347	0.52	negative regulation of NF-kappaB import into nucleus
GO:0008631	0.52	intrinsic apoptotic signaling pathway in response to oxidative stress
GO:0044699	0.50	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:0044424	0.99	intracellular part
GO:0043226	0.90	organelle
GO:0005737	0.90	cytoplasm
GO:0043229	0.89	intracellular organelle
GO:0043227	0.89	membrane-bounded organelle
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0044444	0.87	cytoplasmic part
GO:0005634	0.84	nucleus
GO:0005739	0.78	mitochondrion

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	0.067	1wt6B	0.451	1.84	0.108	0.512	2.7.11.1	NA
2	0.067	1cxzB	0.493	2.05	0.070	0.567	2.7.11.13	NA
3	0.066	1urfA	0.458	3.16	0.038	0.606	2.7.11.13	NA
4	0.060	1qd1B	0.250	4.52	0.008	0.433	2.1.2.5 4.3.1.4	NA
5	0.060	1sc7A	0.548	3.09	0.081	0.701	5.99.1.2	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.03	1i4d1	0.702	3.18	0.105	0.953	0.69	III	complex1.pdb.gz	28,31,34,38,39,41,42,43,45,46,79,82,86,89,90

	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.