D-I-TASSER Q14393-D6

D-I-TASSER results for Q14393-D6

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

Input Sequence in FASTA format

>Q14393 (204 residues)
ERGSFYPGSGFAFYSLDYMRTPLDVGTESTWEVEVVAHIRPAADTGVLFALWAPDLRAVP
LSVALVDYHSTKKLKKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTR
GQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLD
LDEAAYKHSDITAHSCPPVEPAAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| ERGSFYPGSGFAFYSLDYMRTPLDVGTESTWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDYHSTKKLKKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPAAA
Prediction	CCCCCSCCCSSSSSSCCCCCSSCCCCCCCCSSSSSSSSSSSCCCCSSSSSSSCCCCCCCSSSSSSSCCSSSSSSSCCCSSSSSCCSSCCCCCCSCCCCCCSSSSSSSSCCSSSSSSCCCCCCSSCCCCCCCCCCCCCCHHHCCCCCSSSSCCCCCCCCCCCCCCCCCSSSSSSSCCSSSCHHHHHHHCCCCCCCCCCCCCCCCC
Confidence	987513797379996266502025676554159999999827996489998528976422799997577999993796799855501024431235997179999998989999987987502116643233334341432688756882578976678745676120089999999846567676527803688998887789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| ERGSFYPGSGFAFYSLDYMRTPLDVGTESTWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDYHSTKKLKKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPAAA
Prediction	862411343020102353443425354544340402030314442000000125755223000113423332325452120214434444352401344304030314654030303365544424455256434324542545020000001225354343343030002020564413144024434504442113355668
	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                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCSCCCSSSSSSCCCCCSSCCCCCCCCSSSSSSSSSSSCCCCSSSSSSSCCCCCCCSSSSSSSCCSSSSSSSCCCSSSSSCCSSCCCCCCSCCCCCCSSSSSSSSCCSSSSSSCCCCCCSSCCCCCCCCCCCCCCHHHCCCCCSSSSCCCCCCCCCCCCCCCCCSSSSSSSCCSSSCHHHHHHHCCCCCCCCCCCCCCCCC
ERGSFYPGSGFAFYSLDYMRTPLDVGTESTWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDYHSTKKLKKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPAAA

1h30A

0.93

0.85

23.95

1.33

DEthreader

FDGSFYPGSGFAFYSLD-Y-MR-----ST-WEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDY----K--KQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITA-HSCPPVEPA-

1h30A2

0.99

0.93

25.95

2.04

SPARKS-K

ERGSFYPGSGFAFYSLDYMR--------STWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVD-----YHKKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPAAA

1h30A

0.98

0.88

24.73

0.76

MapAlign

ERGSFYPGSGFAFYSL--------DYMRSTWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDYH-----KKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCP-------

1h30A

0.99

0.93

25.95

0.62

CEthreader

ERGSFYPGSGFAFYSLDYMRS--------TWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDYHK-----KQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPAAA

1h30A2

0.98

0.92

25.82

1.72

MUSTER

ERGSFYPGSGFAFYSLDYM--------RSTWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVD-----YHKKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPAAA

1h30A2

0.99

0.90

25.26

2.00

HHsearch

ERGSFYPGSGFAFYSLDYMS---------TWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDQ---------LVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPAAA

1h30A2

0.97

0.91

25.55

2.13

FFAS-3D

ERGSFYPGSGFAFYSLDY--------MRSTWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDYHKKQ-----LVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPAAA

1h30A2

0.90

0.84

23.56

1.18

EigenThreader

ERGSFYPGSGFAFYSLDYMRSTWE--------VEVVAHIRPAADTGVLFALWAD--LRAVPLSVALVDY----HKKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPAAA

1h30A

1.00

0.94

26.22

2.71

CNFpred

ERGSFYPGSGFAFYSLDYMR--------STWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDYH-----KKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPAAA

1h30A2

0.94

0.86

24.22

1.33

DEthreader

ERGSFYPGSGFAFYSLD-Y-MR-----ST-WEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDY----K--KQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITA-HSCPPVEPA-

(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	0.807

(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	1h30A2	0.93	0.60	1.000	0.936	model1_1h30A2.pdb.gz
2	1dykA2	0.73	2.34	0.220	0.824	model1_1dykA2.pdb.gz
3	3asiA	0.73	2.48	0.151	0.843	model1_3asiA.pdb.gz
4	2jd4A	0.72	2.63	0.172	0.853	model1_2jd4A.pdb.gz
5	5mc9A	0.72	2.70	0.202	0.848	model1_5mc9A.pdb.gz
6	2wjsA	0.72	2.81	0.169	0.858	model1_2wjsA.pdb.gz
7	3poyA1	0.70	2.85	0.229	0.828	model1_3poyA1.pdb.gz
8	1q56A	0.70	3.01	0.149	0.853	model1_1q56A.pdb.gz
9	2r16A	0.69	2.74	0.201	0.804	model1_2r16A.pdb.gz
10	1kdkA	0.65	3.22	0.169	0.804	model1_1kdkA.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:0008289	0.88	lipid binding
GO:0005102	0.88	receptor binding
GO:0004866	0.86	endopeptidase inhibitor activity
GO:0060090	0.81	binding, bridging
GO:0043027	0.81	cysteine-type endopeptidase inhibitor activity involved in apoptotic process
GO:0030296	0.81	protein tyrosine kinase activator activity
GO:0005245	0.81	voltage-gated calcium channel activity
GO:0001786	0.81	phosphatidylserine 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:0044699	0.99	single-organism process
GO:0009987	0.92	cellular process
GO:0065007	0.90	biological regulation
GO:0050789	0.90	regulation of biological process
GO:0044763	0.90	single-organism cellular process
GO:0040011	0.87	locomotion
GO:0032501	0.87	multicellular organismal process
GO:0006928	0.87	movement of cell or subcellular component
GO:0050896	0.85	response to stimulus
GO:0050794	0.85	regulation of cellular process
GO:0016477	0.85	cell migration
GO:0016043	0.85	cellular component organization
GO:0048519	0.78	negative regulation of biological process
GO:0048518	0.78	positive regulation of biological process
GO:0080090	0.77	regulation of primary metabolic process
GO:0051239	0.77	regulation of multicellular organismal process
GO:0008152	0.77	metabolic process
GO:0071704	0.76	organic substance metabolic process
GO:0051241	0.76	negative regulation of multicellular organismal process
GO:0051234	0.76	establishment of localization
GO:0048583	0.76	regulation of response to stimulus
GO:0048522	0.76	positive regulation of cellular process
GO:0044237	0.76	cellular metabolic process
GO:0022610	0.76	biological adhesion
GO:0007165	0.76	signal transduction
GO:1901700	0.75	response to oxygen-containing compound
GO:0060255	0.75	regulation of macromolecule metabolic process
GO:0044238	0.75	primary metabolic process
GO:0030198	0.75	extracellular matrix organization
GO:0010033	0.75	response to organic substance
GO:0009605	0.75	response to external stimulus
GO:0002376	0.75	immune system process
GO:0065008	0.74	regulation of biological quality
GO:0051246	0.74	regulation of protein metabolic process
GO:0051128	0.74	regulation of cellular component organization
GO:0048523	0.74	negative regulation of cellular process
GO:0044765	0.74	single-organism transport
GO:0044260	0.74	cellular macromolecule metabolic process
GO:0032879	0.74	regulation of localization
GO:0031323	0.74	regulation of cellular metabolic process
GO:0022607	0.74	cellular component assembly
GO:0016192	0.74	vesicle-mediated transport
GO:0010468	0.74	regulation of gene expression
GO:0002682	0.74	regulation of immune system process
GO:0050900	0.73	leukocyte migration
GO:0050793	0.73	regulation of developmental process
GO:0050766	0.73	positive regulation of phagocytosis
GO:0046907	0.73	intracellular transport
GO:0030162	0.73	regulation of proteolysis
GO:0018193	0.73	peptidyl-amino acid modification
GO:2000026	0.72	regulation of multicellular organismal development
GO:0090002	0.72	establishment of protein localization to plasma membrane
GO:0051704	0.72	multi-organism process
GO:0051093	0.72	negative regulation of developmental process
GO:0042127	0.72	regulation of cell proliferation
GO:0031325	0.72	positive regulation of cellular metabolic process
GO:0010604	0.72	positive regulation of macromolecule metabolic process
GO:0003008	0.72	system process
GO:1902533	0.71	positive regulation of intracellular signal transduction
GO:0051247	0.71	positive regulation of protein metabolic process
GO:0051240	0.71	positive regulation of multicellular organismal process
GO:0048585	0.71	negative regulation of response to stimulus
GO:0045937	0.71	positive regulation of phosphate metabolic process
GO:0010628	0.71	positive regulation of gene expression
GO:0006355	0.71	regulation of transcription, DNA-templated
GO:0001932	0.71	regulation of protein phosphorylation
GO:2000669	0.70	negative regulation of dendritic cell apoptotic process
GO:2000533	0.70	negative regulation of renal albumin absorption
GO:2000352	0.70	negative regulation of endothelial cell apoptotic process
GO:2000270	0.70	negative regulation of fibroblast apoptotic process
GO:1900165	0.70	negative regulation of interleukin-6 secretion
GO:1900142	0.70	negative regulation of oligodendrocyte apoptotic process
GO:0097241	0.70	hematopoietic stem cell migration to bone marrow
GO:0085029	0.70	extracellular matrix assembly
GO:0072661	0.70	protein targeting to plasma membrane
GO:0071333	0.70	cellular response to glucose stimulus
GO:0071307	0.70	cellular response to vitamin K
GO:0070168	0.70	negative regulation of biomineral tissue development
GO:0061098	0.70	positive regulation of protein tyrosine kinase activity
GO:0051897	0.70	positive regulation of protein kinase B signaling
GO:0050711	0.70	negative regulation of interleukin-1 secretion
GO:0048146	0.70	positive regulation of fibroblast proliferation
GO:0046827	0.70	positive regulation of protein export from nucleus
GO:0046813	0.70	receptor-mediated virion attachment to host cell
GO:0046718	0.70	viral entry into host cell
GO:0045892	0.70	negative regulation of transcription, DNA-templated
GO:0043491	0.70	protein kinase B signaling
GO:0043433	0.70	negative regulation of sequence-specific DNA binding transcription factor activity
GO:0043277	0.70	apoptotic cell clearance
GO:0043154	0.70	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0035754	0.70	B cell chemotaxis
GO:0035690	0.70	cellular response to drug
GO:0035457	0.70	cellular response to interferon-alpha
GO:0033159	0.70	negative regulation of protein import into nucleus, translocation
GO:0033138	0.70	positive regulation of peptidyl-serine phosphorylation
GO:0032825	0.70	positive regulation of natural killer cell differentiation
GO:0032720	0.70	negative regulation of tumor necrosis factor production
GO:0032689	0.70	negative regulation of interferon-gamma production
GO:0032148	0.70	activation of protein kinase B activity
GO:0032008	0.70	positive regulation of TOR signaling
GO:0019079	0.70	viral genome replication
GO:0019064	0.70	fusion of virus membrane with host plasma membrane
GO:0018105	0.70	peptidyl-serine phosphorylation
GO:0010804	0.70	negative regulation of tumor necrosis factor-mediated signaling pathway
GO:0003104	0.70	positive regulation of glomerular filtration
GO:0001961	0.70	positive regulation of cytokine-mediated signaling pathway

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:0044421	1.00	extracellular region part
GO:0005615	0.98	extracellular space
GO:0044464	0.93	cell part
GO:0044424	0.91	intracellular part
GO:0005737	0.77	cytoplasm

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	1lclA	0.482	3.30	0.102	0.613	3.1.1.5	100,119
2	0.066	1mveA	0.604	3.53	0.099	0.774	3.2.1.73	NA
3	0.060	1gbgA	0.542	3.48	0.068	0.686	3.2.1.73	NA
4	0.060	3d6eB	0.540	3.16	0.080	0.672	3.2.1.73	NA
5	0.060	3btaA	0.576	3.38	0.054	0.726	3.4.24.69	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	0.05	3d5o3	0.666	3.13	0.129	0.814	0.74	III	complex1.pdb.gz	90,91,110,111,115,120,122
2	0.05	3d5o1	0.666	3.13	0.129	0.814	0.68	III	complex2.pdb.gz	5,7,39,40,41,98,167,168,190,192,194
3	0.03	3fltA	0.678	2.97	0.113	0.824	0.69	OPE	complex3.pdb.gz	47,59,82,152,165

	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.