D-I-TASSER Q9BZF9-D4

D-I-TASSER results for Q9BZF9-D4

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

Input Sequence in FASTA format

>Q9BZF9 (128 residues)
EKKLEMEKLLLENDSLSKDVSRLETVFVPPEKHEKEIIALKSNIVELKKQLSELKKKCGE
DQEKIHALTSENTNLKKMMSNQYVPVKTHEEVKMTLNDTLAKTNRELLDVKKKFEDINQE
FVKIKDKN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| EKKLEMEKLLLENDSLSKDVSRLETVFVPPEKHEKEIIALKSNIVELKKQLSELKKKCGEDQEKIHALTSENTNLKKMMSNQYVPVKTHEEVKMTLNDTLAKTNRELLDVKKKFEDINQEFVKIKDKN
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	82579999999999999999999875201588999999999999999999999999999899999999999999999998735469999999999999999999999999999999999999976259
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| EKKLEMEKLLLENDSLSKDVSRLETVFVPPEKHEKEIIALKSNIVELKKQLSELKKKCGEDQEKIHALTSENTNLKKMMSNQYVPVKTHEEVKMTLNDTLAKTNRELLDVKKKFEDINQEFVKIKDKN
Prediction	85644355045546414641540444334475355425515643451463155046425644541451445345246415654443542563455145315514542462465265355414515788
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
EKKLEMEKLLLENDSLSKDVSRLETVFVPPEKHEKEIIALKSNIVELKKQLSELKKKCGEDQEKIHALTSENTNLKKMMSNQYVPVKTHEEVKMTLNDTLAKTNRELLDVKKKFEDINQEFVKIKDKN

6irdB

0.14

4.80

1.33

DEthreader

TMKLHCTQVDKIVAQYDKEKSTHEKILIKKETEIKIQTLTTDHKSKVKEIVAQHTKEWSEMINTHSAEEQEIRDLHLSQQCELLRKLLINAHEQQTQQLKLSHDRESKEMRAHQAKISMENSKAISQD

3na7A1

0.14

0.13

4.52

1.20

FFAS-3D

--EPLIREKRKDLDKALNDKEAKNK---AILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKMSEIKRELRSLNIEEDIAKERSNQANREIENLQNEIKRKSEKQEDLKKEMLELEKLALEL----

4ke2A

0.04

2.00

1.33

DEthreader

DTAAAASAAAAAVASAAKAL-ET--I-N---VKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP

6yvuB

0.12

4.38

0.86

SPARKS-K

STLEKISSSNKDLEDEKMKFQESLKKVDQRKEIKDRISSCSSKEKTLVLERRELEGTRVSLEERTKNLVSKMEKAEKTLKSTKHSISEAENMLEELRGQQTEHETEIKDLTQLLEKERSILDDIKLSL

3pltA

0.06

2.69

0.71

MapAlign

EKGVLRAMEVVASERREAAKQLSLWGANDDDVSDVTDKLGVLIYELGELQDQFIDKYDQYRVTLKSIRNIEASVQPSRDRKAEAESLVAEAQLSNITREKLKAAYSYMFDSLRELSEKFALIAGYGKA

6z9lA4

0.09

3.53

0.48

CEthreader

AKENALKDKQAATKQAQNTLDNSKEEMKSKEELQQEIASNQEKLATAQQAESDAQQARSASQQALNTAKTTQATAEKELSVHKATLANLQAVATKSTTNYEEKVRQTATAEKSLQQTKDQLATINELI

4rsiB

0.16

5.20

0.81

MUSTER

PWDLQLQEKESQIQLAESELSLLEET---QAKLKKNVETLEEKILAKKTHKQELQDLILDLKKKLNSLKDERSQGEKNFTSAHLKLKEMQKVLNAHRQRAMEARSSLSKAQNKSKVLTALSRLQKSGR

6z6fD

0.12

4.38

0.84

HHsearch

ELEVENNLKFSQIETLEKDIETLKGSLSKTDNVQDEIEKEERVSVSRDTEKKYMEQEIKRAVDATHKLNEKQNGLESELKLKFEKSEELNEKIGFLKKELKLENDLNEELVGQLSKTMDNLENLTIPR

2efrA

0.20

6.24

1.18

FFAS-3D

ELLSKNYHLENEVARLKKLLERAEE---RAELSEGKSAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYKAISEEMKQLEDK-

5nnvA

0.09

3.31

0.55

EigenThreader

ELSKQEAVFETLQAEVKQLRAQVKEKQQLSNELTELKIAAAKKEQACKGEEDNLARLKKELTETELALKEA-KEDLSFLTSESSSTSGEEKLEEAAKHKLNDKTKTIELIALRRDQRIKLQHGLDTYE

(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	0.5031

(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	6sz9D	0.77	2.98	0.070	1.000	model1_6sz9D.pdb.gz
2	2d4cB	0.76	2.79	0.102	1.000	model1_2d4cB.pdb.gz
3	2r02A2	0.76	2.85	0.102	0.992	model1_2r02A2.pdb.gz
4	1y2oA	0.74	2.91	0.070	1.000	model1_1y2oA.pdb.gz
5	3ok8A	0.71	3.10	0.071	0.953	model1_3ok8A.pdb.gz
6	2d1lA	0.69	3.14	0.113	0.953	model1_2d1lA.pdb.gz
7	4akkA2	0.49	3.34	0.060	0.672	model1_4akkA2.pdb.gz
8	2xciA	0.39	5.06	0.043	0.688	model1_2xciA.pdb.gz
9	3rauA1	0.39	2.77	0.040	0.492	model1_3rauA1.pdb.gz
10	4lsbA	0.35	4.92	0.041	0.609	model1_4lsbA.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	0.31	heterocyclic compound binding
GO:0097159	0.31	organic cyclic compound 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	0.90	biological regulation
GO:0050789	0.90	regulation of biological process
GO:0050794	0.88	regulation of cellular process
GO:0048518	0.80	positive regulation of biological process
GO:0048522	0.79	positive regulation of cellular process
GO:0007165	0.79	signal transduction
GO:0050896	0.78	response to stimulus
GO:0060255	0.76	regulation of macromolecule metabolic process
GO:0051716	0.76	cellular response to stimulus
GO:0031323	0.76	regulation of cellular metabolic process
GO:0080090	0.75	regulation of primary metabolic process
GO:0065009	0.75	regulation of molecular function
GO:0009966	0.75	regulation of signal transduction
GO:0050790	0.74	regulation of catalytic activity
GO:0048523	0.74	negative regulation of cellular process
GO:1902531	0.73	regulation of intracellular signal transduction
GO:0051247	0.73	positive regulation of protein metabolic process
GO:0044093	0.73	positive regulation of molecular function
GO:0035556	0.73	intracellular signal transduction
GO:0032268	0.73	regulation of cellular protein metabolic process
GO:0031325	0.73	positive regulation of cellular metabolic process
GO:0006950	0.73	response to stress
GO:0051049	0.72	regulation of transport
GO:0043085	0.72	positive regulation of catalytic activity
GO:0033554	0.72	cellular response to stress
GO:0032270	0.72	positive regulation of cellular protein metabolic process
GO:0080134	0.71	regulation of response to stress
GO:0051336	0.71	regulation of hydrolase activity
GO:0009968	0.71	negative regulation of signal transduction
GO:1902532	0.70	negative regulation of intracellular signal transduction
GO:0097193	0.70	intrinsic apoptotic signaling pathway
GO:0090316	0.70	positive regulation of intracellular protein transport
GO:0051345	0.70	positive regulation of hydrolase activity
GO:0042981	0.70	regulation of apoptotic process
GO:0010942	0.70	positive regulation of cell death
GO:0009416	0.70	response to light stimulus
GO:0006974	0.70	cellular response to DNA damage stimulus
GO:0050728	0.69	negative regulation of inflammatory response
GO:0043280	0.69	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0042347	0.69	negative regulation of NF-kappaB import into nucleus
GO:0042307	0.69	positive regulation of protein import into nucleus
GO:0009411	0.69	response to UV
GO:0008631	0.69	intrinsic apoptotic signaling pathway in response to oxidative stress
GO:0008630	0.69	intrinsic apoptotic signaling pathway in response to DNA damage
GO:0044699	0.54	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:0005634	1.00	nucleus

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	0.066	1cxzB	0.482	1.89	0.070	0.562	2.7.11.13	NA
2	0.066	1urfA	0.474	2.98	0.128	0.609	2.7.11.13	NA
3	0.066	1a91A	0.457	2.62	0.090	0.602	3.6.3.14	NA
4	0.060	2b5uA	0.608	2.93	0.031	0.797	3.1.-.-	NA
5	0.060	1dcnB	0.582	3.41	0.098	0.828	4.3.2.1	73,74

	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:

No Binding sites was predicted

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

	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.