D-I-TASSER P17813-D4

D-I-TASSER results for P17813-D4

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

Input Sequence in FASTA format

>P17813 (216 residues)
LNMDSLSFQLGLYLSPHFLQASNTIEPGQQSFVQVRVSPSVSEFLLQLDSCHLDLGPEGG
TVELIQGRAAKGNCVSLLSPSPEGDPRFSFLLHFYTVPIPKTGTLSCTVALRPKTGSQDQ
EVHRTVFMRLNIISPDLSGCTSKGLVLPAVLGITFGAFLIGALLTAALWYIYSHTRSPSK
REPVVAVAAPASSESSSTNHSIGSTQSTPCSTSSMA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| LNMDSLSFQLGLYLSPHFLQASNTIEPGQQSFVQVRVSPSVSEFLLQLDSCHLDLGPEGGTVELIQGRAAKGNCVSLLSPSPEGDPRFSFLLHFYTVPIPKTGTLSCTVALRPKTGSQDQEVHRTVFMRLNIISPDLSGCTSKGLVLPAVLGITFGAFLIGALLTAALWYIYSHTRSPSKREPVVAVAAPASSESSSTNHSIGSTQSTPCSTSSMA
Prediction	CCCCCSSSSSSSSCCCCCCCCCCSSSCCCSSSSSSSSCCCCCCCSSSSSSSSSCCCCCCCCSSSSSCCCCCCCSSSSSCCCCCCCCSSSSSSSSSSCCCCCSSSSSSSSSSSCCCCCCCCCCCCCSCCCCCSCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	965654899997458443556627815974899999716897607999899810799998458863577787558852479988524899998651356505899999998137788775545531346310158988755568763112356799999999999998850122578667543455689998755432223366667887666689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| LNMDSLSFQLGLYLSPHFLQASNTIEPGQQSFVQVRVSPSVSEFLLQLDSCHLDLGPEGGTVELIQGRAAKGNCVSLLSPSPEGDPRFSFLLHFYTVPIPKTGTLSCTVALRPKTGSQDQEVHRTVFMRLNIISPDLSGCTSKGLVLPAVLGITFGAFLIGALLTAALWYIYSHTRSPSKREPVVAVAAPASSESSSTNHSIGSTQSTPCSTSSMA
Prediction	763641403021143651443434054645010102034425401020330203355636414004630244301422445474442121103334343343130302010224466664532541334141434546534441132110332031122110220210110102235446444144454445454343433343444332445568
	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                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCSSSSSSSSCCCCCCCCCCSSSCCCSSSSSSSSCCCCCCCSSSSSSSSSCCCCCCCCSSSSSCCCCCCCSSSSSCCCCCCCCSSSSSSSSSSCCCCCSSSSSSSSSSSCCCCCCCCCCCCCSCCCCCSCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
LNMDSLSFQLGLYLSPHFLQASNTIEPGQQSFVQVRVSPSVSEFLLQLDSCHLDLGPEGGTVELIQGRAAKGNCVSLLSPSPEGDPRFSFLLHFYTVPIPKTGTLSCTVALRPKTGSQDQEVHRTVFMRLNIISPDLSGCTSKGLVLPAVLGITFGAFLIGALLTAALWYIYSHTRSPSKREPVVAVAAPASSESSSTNHSIGSTQSTPCSTSSMA

3qw9A

0.17

0.10

3.37

0.83

DEthreader

-PNSNATFNMELYNTDLFVPSPFSVAENEHVYVEVSVTKADQDLGFAIQTCFLSPYSNRMSYTIIENICPKDDSVKFYSSKRVDKKRFSFLFKSVFN-TSL-LFLHCELTLCSRKKGKLPTMNKKTFTKPLAVVL-Q-------------------------------------------------------------------------------

3qw9A

0.19

0.13

4.19

1.73

SPARKS-K

-PNSNATFNMELYNTDLFLVPSPSVAENEHVYVEVSVTKADQDLGFAIQTCFLSPYSNPDRYTIIENICPKDDSVKFYSSKRVHKKRFSFLFK--SVFNTSLLFLHCELTLCSRKKGSLKLPRCVTPDDACMIWTMMQNKKTFTKPLAVVLQ----------------------------------------------------------------

3qw9A

0.20

0.12

3.86

0.89

MapAlign

-PNSNATFNMELYNTDLFLVPSFSVAENEHVYVEVSVTKADQDLGFAIQTCFLSPYPDRMSYTIIENICPKDDSVKFYSSKEVDKKRFSFLFKSV--FNTSLLFLHCELTLCSRKKLPRCVNKKTFTKPLAVVL----------------------------------------------------------------------------------

4wrnA2

0.15

0.10

3.26

0.77

CEthreader

GGTGMFTVRMALFQTPSYTQPYVTLSTEAFLYVGTMLDGGLSRFALLMTNCYATPSSQALKYFIIQDRCPHTSTIQVVENGESSQGRFSVQMFRF-AGNYDLVYLHCEVYLCDTMNEKCKPIDQSRVLNLGPITRKGVQ-----------------------------------------------------------------------------

3qw9A

0.19

0.13

4.20

1.29

MUSTER

-PNSNATFNMELYNTDLFLVPSPGVAENEHVYVEVSVTKADQDLGFAIQTCFLSPYSNPDRYTIIENICPKDDSVKFYSSKRVHKKRFSFLFKS--VFNTSLLFLHCELTLCSRKKGSLK-LPRCVTPDDACTSLDATMIWTMMQNKKTFTKLAV-------------------------------------------------------------

3qw9A

0.18

0.11

3.61

3.81

HHsearch

-PNSNATFNMELYNTDLFLVPSGVVAENEHVYVEVSVTKADQDLGFAIQTCFLSPYSNPSDYTIIENICPKDDSVKFYSHAEVDKKRFSF-LFKSVF-NTSLLFLHCELTLCSRKKGSLKLSLTKTF--TKPLVLQ--------------------------------------------------------------------------------

3qw9A

0.16

0.09

2.91

1.28

FFAS-3D

---SNATFNMELYNTDLFLVPSPSVAENEHVYVEVSVTKADQDLGFAIQTCFLSPYSNPDRYTIIENICPKDDSVKFYSSFPIPHAEVDKKRFSFLFKSTSLLFLHCELTLCSRKKGSL-------------------------------------------------------------------------------------------------

3qw9A

0.20

0.12

3.87

0.77

EigenThreader

-PNSNATFNMELYNTDLFLVPVFSVAENEHVYVEVSVTKADQDLGFAIQTCFLSPYSNPDRMTIIENICPKDDSVKFYSSKIPHKKRFSFLFK--SVFNTSLLFLHCELLCSRKKGSLKLPRCKKTFTKPLAVVLQ--------------------------------------------------------------------------------

3qw9A

0.21

0.11

3.39

1.33

CNFpred

-PNSNATFNMELYNTDLFLVPSFSVAENEHVYVEVSVTKADQDLGFAIQTCFLSPYS-MSDYTIIENICPKDDSVKFYSSKRVDKKRFSFLFKSVF--NTSLLFLHCELTLCSRKK----------------------------------------------------------------------------------------------------

4wrnA2

0.15

0.09

3.10

0.83

DEthreader

GGTGMFTVRMALFQTPSYTQPYVTLSTEAFLYVGTMLDGGDSRFALLMTNCYATPSSDPLKYFIIQDRCPHTDTIQVVENGESSQGRFSVQMRAGNY--DL-VYLHCEVYLCDTMNE----DSRVLNLGPITRKGV--Q-----------------------------------------------------------------------------

(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	0.5992

(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	3qw9A	0.56	1.89	0.189	0.611	model1_3qw9A.pdb.gz
2	4wrnA	0.53	3.01	0.156	0.616	model1_4wrnA.pdb.gz
3	3weuA	0.52	5.16	0.074	0.829	model1_3weuA.pdb.gz
4	6bywB1	0.52	4.93	0.069	0.815	model1_6bywB1.pdb.gz
5	5bupA	0.52	2.27	0.127	0.583	model1_5bupA.pdb.gz
6	3nk3A2	0.49	2.96	0.149	0.569	model1_3nk3A2.pdb.gz
7	1peuA	0.37	6.47	0.051	0.727	model1_1peuA.pdb.gz
8	2b3bA	0.34	6.02	0.073	0.625	model1_2b3bA.pdb.gz
9	2heuA	0.33	6.07	0.049	0.593	model1_2heuA.pdb.gz
10	2uvhA	0.31	6.45	0.051	0.602	model1_2uvhA.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:0004871	0.91	signal transducer activity
GO:0005102	0.87	receptor binding
GO:0005126	0.86	cytokine receptor binding
GO:0005160	0.85	transforming growth factor beta receptor binding
GO:0003824	0.84	catalytic activity
GO:0016740	0.82	transferase activity
GO:0004872	0.82	receptor activity
GO:0019199	0.81	transmembrane receptor protein kinase activity
GO:0004674	0.81	protein serine/threonine kinase activity
GO:0005024	0.80	transforming growth factor beta-activated receptor activity
GO:0005114	0.78	type II transforming growth factor beta receptor binding
GO:0097367	0.73	carbohydrate derivative binding
GO:0005539	0.70	glycosaminoglycan binding
GO:0050431	0.50	transforming growth factor beta 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:0050794	1.00	regulation of cellular process
GO:0044699	0.94	single-organism process
GO:0009987	0.94	cellular process
GO:0044767	0.92	single-organism developmental process
GO:0044763	0.92	single-organism cellular process
GO:0048522	0.88	positive regulation of cellular process
GO:0060255	0.85	regulation of macromolecule metabolic process
GO:0048856	0.84	anatomical structure development
GO:0010468	0.84	regulation of gene expression
GO:0010604	0.78	positive regulation of macromolecule metabolic process
GO:0010628	0.77	positive regulation of gene expression
GO:0048513	0.72	animal organ development
GO:0031323	0.71	regulation of cellular metabolic process
GO:0080090	0.70	regulation of primary metabolic process
GO:0051239	0.69	regulation of multicellular organismal process
GO:0048583	0.69	regulation of response to stimulus
GO:0010556	0.69	regulation of macromolecule biosynthetic process
GO:0009966	0.68	regulation of signal transduction
GO:0017015	0.67	regulation of transforming growth factor beta receptor signaling pathway
GO:0050896	0.66	response to stimulus
GO:0031325	0.63	positive regulation of cellular metabolic process
GO:0051246	0.62	regulation of protein metabolic process
GO:0019220	0.62	regulation of phosphate metabolic process
GO:0051240	0.61	positive regulation of multicellular organismal process
GO:0010557	0.61	positive regulation of macromolecule biosynthetic process
GO:0001934	0.61	positive regulation of protein phosphorylation
GO:0007165	0.59	signal transduction
GO:0016043	0.55	cellular component organization
GO:0009628	0.55	response to abiotic stimulus
GO:0048869	0.52	cellular developmental process
GO:0009653	0.52	anatomical structure morphogenesis
GO:0048519	0.51	negative regulation of biological process
GO:0048523	0.50	negative regulation of cellular process
GO:0007179	0.50	transforming growth factor beta receptor signaling pathway
GO:0001837	0.50	epithelial to mesenchymal transition

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:0044464	1.00	cell part
GO:0044425	0.76	membrane part
GO:0044424	0.75	intracellular part
GO:0044421	0.64	extracellular region part
GO:0005615	0.59	extracellular space
GO:0031224	0.58	intrinsic component of membrane
GO:0016021	0.57	integral component of membrane
GO:0044446	0.55	intracellular organelle part
GO:0005737	0.53	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	0.060	2dewX	0.409	4.80	0.034	0.597	3.5.3.15	NA
2	0.060	1wmrA	0.441	4.99	0.066	0.685	3.2.1.57	NA
3	0.060	2vtcA	0.426	4.58	0.037	0.607	3.2.1.4	NA
4	0.060	3ciaA	0.419	5.40	0.057	0.690	3.4.11.-	NA
5	0.060	1wd9A	0.402	4.81	0.034	0.593	3.5.3.15	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	0.02	3nk3B	0.481	2.83	0.149	0.556	0.56	III	complex1.pdb.gz	6,8,9,10,11,12,23,24,25,26,27,31,33,57,92,93,94,101,102,103,104,105,106,107,108,109,110,111
2	0.01	3oklB	0.441	3.86	0.022	0.574	0.58	UUU	complex2.pdb.gz	51,64,68,107,109
3	0.01	1m7iB	0.431	4.07	0.038	0.574	0.66	UUU	complex3.pdb.gz	54,56,104,106,128
4	0.01	1uz8H	0.434	3.93	0.038	0.565	0.55	UUU	complex4.pdb.gz	58,103,104
5	0.01	2g5bB	0.433	3.96	0.027	0.569	0.59	UUU	complex5.pdb.gz	55,102,104,106,107,129

	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.