D-I-TASSER Q9UPR3-D3

D-I-TASSER results for Q9UPR3-D3

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

Input Sequence in FASTA format

>Q9UPR3 (188 residues)
VPAFQSDGTDEPESKEPVEKEEEPDPEPPPVTPQVGEGRKSRKFSRLSCLRRRRHPPKVG
DDSDLSEGFESDSSHDSARASEGSDSGSDKSLEGGGTAFDAETDSEMNSQESRSDLEDME
EEEGTRSPTLEPPRGRSEAPDSLNGPLGTTNPHTSASHRPCVNGDVDKPSEPASEEGSES
EGSESSGR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| VPAFQSDGTDEPESKEPVEKEEEPDPEPPPVTPQVGEGRKSRKFSRLSCLRRRRHPPKVGDDSDLSEGFESDSSHDSARASEGSDSGSDKSLEGGGTAFDAETDSEMNSQESRSDLEDMEEEEGTRSPTLEPPRGRSEAPDSLNGPLGTTNPHTSASHRPCVNGDVDKPSEPASEEGSESEGSESSGR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	98755688877442343223467888887777775433344455521123331155555654322356666656676667777655665555566544565446555443333432223323356775335532235788766887777776433334433467667886432233441010121369
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| VPAFQSDGTDEPESKEPVEKEEEPDPEPPPVTPQVGEGRKSRKFSRLSCLRRRRHPPKVGDDSDLSEGFESDSSHDSARASEGSDSGSDKSLEGGGTAFDAETDSEMNSQESRSDLEDMEEEEGTRSPTLEPPRGRSEAPDSLNGPLGTTNPHTSASHRPCVNGDVDKPSEPASEEGSESEGSESSGR
Prediction	74545665475563655454656474744745555665555753542533455545664645543554454545654465462455555555754554444535564555545543663655646654554445557545654644444545443444452454636655545567445566446688
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
VPAFQSDGTDEPESKEPVEKEEEPDPEPPPVTPQVGEGRKSRKFSRLSCLRRRRHPPKVGDDSDLSEGFESDSSHDSARASEGSDSGSDKSLEGGGTAFDAETDSEMNSQESRSDLEDMEEEEGTRSPTLEPPRGRSEAPDSLNGPLGTTNPHTSASHRPCVNGDVDKPSEPASEEGSESEGSESSGR

6hwjA1

0.07

0.06

2.64

0.54

CEthreader

---------------MTPNWSELVAAADPALVLPSGERRAEVAVPGPLRLDALLDLGEGHAVGVVRSARWTVPLVRDGAGGVRRSRPGDGTAEHLVAALARDAAFVLEAFTGAAPVTGERGIIVDESVIVGECAVVKWAVRLPAEGEPGSPAAQRIAALARGGFTEMPRPWGLLTLAEGAQASVVAYL

6vbyA

0.10

3.73

0.47

EigenThreader

AGAPVVGNWLQVGDDLNHRNLMSLAKRFGDVLHTQGVEFGSRTRRRLQLMMYNDMFRIMFDTRFESEQDGEINHDNVLYIVENINVAAIETTLWSIEWGIAELVNHPAIQSKLREEMDSVLGAGVPVTEPDLERLPYLQAIVKETLRLRMAIPLLVPAWFLANDPKRWVEAHGNDFRFVPFGVGRRSC

3cnfB

0.11

3.87

0.42

FFAS-3D

TVLRYDDQIDIEAFRWSRYFLDELQLRRLSVGLRLITNPRIARRFNGVRIMYLTDPEGYVAVQYAHRLFSSSLANKRNRVTYTHPPTGMAYPSPTGVHMTINERAGMSKLVADNDILDIETQHVDAESIMTAPKGKLFHLQFMDGLLRPEASGSMRAIVNHNEVDRPREMDTGTRNGDLLYSPVANGQ

4nl6A

0.09

3.30

1.47

SPARKS-K

GQSDDSDIWDDTALKNGDICETSGKPKTTPKRKPAKKNKSQKKNTAASLQQWKVGDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICEVANNIEQNAQENENESQVSTDESENSPGNKSDNIKPKSAPWNSFLPPPPPMPGPRLGPGKPGLKFNGPPPPPPPPPPHLLS

3j04A

0.14

0.04

1.46

0.62

CNFpred

---------VTRQEEEMQAKDEELQRTKERQQKAEAELKELEQ----------KHTQLCEEKNLLQEKLQAETELYA---------------------------------------------------------------------------------------------------------------

6vkzA

0.09

0.06

2.43

0.67

DEthreader

----------------------EKYYDEPSLTPYSSDTQIVFYMMYYINDQTALKLPEIESIDILDDIYLNFMIFEPEDDLERIW----DFLD-F-YQPYFLDEKYLVRT-PSQMPLIKTIC-------------------IKGVRKVTASCITFNVCTSRERLDE-DPFNSVVYVHECARD------

6n8pA

0.06

0.05

2.10

0.79

MapAlign

-------------------------------WDLQGSRVLYHFLSSQQLENIWWQRDGRLLVSCHSDGSYCQWPVSSEAQQPEPLRSLVPYGPFPCKAITRILWLTTRQGLPFTIFQGGMPRASYGDRHCISVIHDGQQ----TAFDFTSRVIGFTVLTEADPAATFDDPYALVVLAEEELVVIDLQ-

6etxG

0.07

3.01

0.96

MUSTER

LFLSLKASYRLHQLRSWGAPEGESHQRYLRNKDFLLGVNFPLSFPNLCSCPLLKSLVFSSHCKAVSGYSDQVVHQRRSATSSLRRCLLTELPSFLCVASPRVTAVPLDSYCNDRSAEYERRVLKEGGSLAAKQCLLNGAPELAA-DWLNRRSQFFPEPAGGLWSIRPQNGWSFIRIPGKESLITDSGK

2dcoA

0.26

0.05

1.47

0.58

HHsearch

-----------------------------------------------------------------------------------------------GSY-D----------AYRTDCEE-----------LSGARTFRLAPAQWSCRETFQA-------------------------------------

6eojD

0.09

3.30

0.54

CEthreader

AAHTESIRDMAFSSNDSKFVTCSDDNILKIWNFSNGKQERVLSGHHWDVKSCDWHPEMGLIASASKDNLVKLWDPRSGNCISSILKFKHTVLKTRMAISKDKSCMCVRDETDYMTLEWHPINESMFTLACYDGKHFDLLQNLNEPILTIPYAHDKCITSLSYNPVGHIFATAAKDRTIRFWTRARPID

(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	0.4608

(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	4ug4A	0.43	5.59	0.036	0.755	model1_4ug4A.pdb.gz
2	1wdlA	0.43	4.99	0.025	0.702	model1_1wdlA.pdb.gz
3	2y8nA	0.42	5.90	0.040	0.777	model1_2y8nA.pdb.gz
4	4c5yA	0.42	5.85	0.046	0.777	model1_4c5yA.pdb.gz
5	5fauA	0.42	5.96	0.066	0.777	model1_5fauA.pdb.gz
6	2dewX	0.42	5.56	0.056	0.729	model1_2dewX.pdb.gz
7	2vqrA	0.38	5.79	0.006	0.681	model1_2vqrA.pdb.gz
8	1n2lA	0.36	5.71	0.052	0.644	model1_1n2lA.pdb.gz
9	1fsuA	0.36	5.94	0.058	0.665	model1_1fsuA.pdb.gz
10	2vhlB	0.35	6.25	0.066	0.702	model1_2vhlB.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:0070182	1.00	DNA polymerase binding
GO:0051721	1.00	protein phosphatase 2A binding
GO:0042826	1.00	histone deacetylase binding
GO:0042162	1.00	telomeric DNA binding
GO:0031625	1.00	ubiquitin protein ligase binding
GO:0003723	0.59	RNA 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	0.88	cellular process
GO:0065007	0.87	biological regulation
GO:0050789	0.87	regulation of biological process
GO:0080090	0.86	regulation of primary metabolic process
GO:0060255	0.86	regulation of macromolecule metabolic process
GO:0031323	0.86	regulation of cellular metabolic process
GO:0008152	0.86	metabolic process
GO:0035303	0.85	regulation of dephosphorylation
GO:0032204	0.85	regulation of telomere maintenance
GO:0044237	0.84	cellular metabolic process
GO:0071704	0.77	organic substance metabolic process
GO:0043170	0.76	macromolecule metabolic process
GO:0044260	0.75	cellular macromolecule metabolic process
GO:0044238	0.74	primary metabolic process
GO:0034641	0.73	cellular nitrogen compound metabolic process
GO:0090304	0.56	nucleic acid metabolic process
GO:0016070	0.55	RNA metabolic process
GO:0016071	0.53	mRNA metabolic process
GO:0051028	0.52	mRNA transport
GO:0031326	0.51	regulation of cellular biosynthetic process
GO:0010556	0.51	regulation of macromolecule biosynthetic process
GO:0006406	0.51	mRNA export from nucleus
GO:0000956	0.51	nuclear-transcribed mRNA catabolic process
GO:2000112	0.50	regulation of cellular macromolecule biosynthetic 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:0005737	1.00	cytoplasm
GO:0005634	1.00	nucleus
GO:0044444	0.82	cytoplasmic part
GO:0005829	0.72	cytosol

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	1mioA	0.398	5.52	0.058	0.707	1.18.6.1	NA
2	0.060	2q3uA	0.407	5.32	0.048	0.686	3.5.3.12	87
3	0.060	2dewX	0.416	5.56	0.056	0.729	3.5.3.15	NA
4	0.060	2gamC	0.404	5.77	0.040	0.745	2.4.1.102	86
5	0.060	2jerD	0.406	5.47	0.035	0.702	3.5.3.12	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	0.01	1r27B	0.407	5.22	0.037	0.686	0.43	F3S	complex1.pdb.gz	100,101,102,103,104,137

	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.