D-I-TASSER Q9UKN5-D2

D-I-TASSER results for Q9UKN5-D2

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

Input Sequence in FASTA format

>Q9UKN5 (104 residues)
ERNYTLPPPPYPHLESSYFRTILPGILSYLADRPPPQYIHPNSINVDGNTALSITNNPSA
LDPYQSNGNVGLEPGIVSIDSRSVNTHGAQSLHPSDGHEVALDT

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| ERNYTLPPPPYPHLESSYFRTILPGILSYLADRPPPQYIHPNSINVDGNTALSITNNPSALDPYQSNGNVGLEPGIVSIDSRSVNTHGAQSLHPSDGHEVALDT
Prediction	CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCSSSSCC
Confidence	99888998898752136788885889987346999864588852357983144158988789888999755445612234431267886555889971465059
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| ERNYTLPPPPYPHLESSYFRTILPGILSYLADRPPPQYIHPNSINVDGNTALSITNNPSALDPYQSNGNVGLEPGIVSIDSRSVNTHGAQSLHPSDGHEVALDT
Prediction	86737254443442444214311320142047443353244541425443424245546424425464434144222414444245644541455744534368
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCSSSSCC
ERNYTLPPPPYPHLESSYFRTILPGILSYLADRPPPQYIHPNSINVDGNTALSITNNPSALDPYQSNGNVGLEPGIVSIDSRSVNTHGAQSLHPSDGHEVALDT

2hlwA

0.07

2.77

0.57

CEthreader

EGRLEPRKFHCKGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMT-----LTRWTGMIIGPPRTIYENRIYSLKIEFVRFVTKINMNGVNSSNGVVDPRA

6tnfB3

0.06

2.56

0.57

EigenThreader

AEEADINVTEKLLDPGSQQFLQFLTWTVKICKENALELAQDIHACLGDIDQDVEIESRSHFAIVNVKTAAPTVCLLVLGQADKVLEETIQTFHELVQTALPAGS

3iz5E

0.09

3.31

0.32

FFAS-3D

-RSFGIRRNEKIACYVTIRGEKAMQLLESGLKVKEYE-LLRRNFSDTGCFGFGIQEHIDLGMKYDPSTGIGMDFFVVERAGYRVSRRRRCKARVGIHQRVTKE-

4nzrM1

0.10

3.54

0.94

SPARKS-K

GSYQSEIDLSGGANFREKFRNFANELSEAITNRPVPK-TEISGLIKTGDNFITPSFKAGYYDHVASDGS----LLSYYQSTEYFNNRVLMPILQTTNGTLMAN-

5osmA

0.19

0.08

2.48

0.41

CNFpred

-------------LIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLA-------------------------------------------------

3psfA

0.07

0.06

2.37

0.83

DEthreader

VENFLAQADIQDISQEVKDNLTKNCQKLVAKTVKFMKLLYANL-------------TSEEVRSLIHPQNLSSELSWETFIVLVSVEVKATALKGKRK-------

3tigA

0.07

0.06

2.41

0.58

MapAlign

-----------DKLCRKASLVKLSSFNKKKENEEGNFDIRSWVLVDNQYNIYLYFQLFGFDFMVDKNLKVWLIEVNGAPACAQKLYAELCKGIVDLAISS----

2rcjT

0.17

0.15

5.08

0.54

MUSTER

LGQPKANPTVTLFPPSS---EELQATLVCLISDFYPGAVT--AWKADGSP---VKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSQVTHEGSTVEKTVAP

4oj5A3

0.20

0.12

3.70

0.43

HHsearch

------------------------------------VYLNAGESVITSNTELPMVVGPGSLKANSGSSFLIKAGGTLSLI-------GLSGISTDGGHMFRVST

2h2yA

0.11

0.10

3.51

0.56

CEthreader

PSRTVEKHIKTKYNLGNANYRIQKELNNFLKNPPINCTIDVHPSN---------IRIWIVQYVGLENTIYANEVYKIKIIIVYFLQKPPKHTHVYSNGDICLSV

(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	0.5357

(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	6nbqD	0.48	4.69	0.029	0.827	model1_6nbqD.pdb.gz
2	7astM	0.48	4.46	0.058	0.856	model1_7astM.pdb.gz
3	1a6eB	0.48	3.86	0.073	0.740	model1_1a6eB.pdb.gz
4	5wkrA	0.47	3.44	0.049	0.721	model1_5wkrA.pdb.gz
5	6u5oL	0.47	4.53	0.077	0.817	model1_6u5oL.pdb.gz
6	7lumJ	0.47	3.87	0.036	0.740	model1_7lumJ.pdb.gz
7	1e6vB	0.46	3.71	0.077	0.731	model1_1e6vB.pdb.gz
8	1jx0A	0.46	3.46	0.037	0.702	model1_1jx0A.pdb.gz
9	3p9dH2	0.46	4.20	0.036	0.760	model1_3p9dH2.pdb.gz
10	5nd5A	0.46	4.07	0.046	0.750	model1_5nd5A.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:0019899	0.68	enzyme binding
GO:1990226	0.67	histone methyltransferase 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	1.00	single-organism process
GO:0009987	1.00	cellular process
GO:0008152	0.63	metabolic process
GO:0071704	0.62	organic substance metabolic process
GO:0044238	0.61	primary metabolic process
GO:0044237	0.60	cellular metabolic process
GO:0043170	0.60	macromolecule metabolic process
GO:0044260	0.59	cellular macromolecule metabolic process
GO:0034641	0.57	cellular nitrogen compound metabolic process
GO:0007165	0.57	signal transduction
GO:1901576	0.56	organic substance biosynthetic process
GO:0090304	0.56	nucleic acid metabolic process
GO:0044763	0.56	single-organism cellular process
GO:0044249	0.56	cellular biosynthetic process
GO:0060255	0.55	regulation of macromolecule metabolic process
GO:0034645	0.55	cellular macromolecule biosynthetic process
GO:0032774	0.55	RNA biosynthetic process
GO:0019538	0.55	protein metabolic process
GO:0016043	0.55	cellular component organization
GO:0006351	0.54	transcription, DNA-templated
GO:0010468	0.53	regulation of gene expression
GO:0006464	0.53	cellular protein modification process
GO:0006325	0.53	chromatin organization
GO:0050896	0.52	response to stimulus
GO:0048519	0.52	negative regulation of biological process
GO:0048523	0.51	negative regulation of cellular process
GO:0043985	0.51	histone H4-R3 methylation
GO:0042221	0.51	response to chemical
GO:0008283	0.51	cell proliferation
GO:0006366	0.51	transcription from RNA polymerase II promoter
GO:0071363	0.50	cellular response to growth factor stimulus
GO:0051726	0.50	regulation of cell cycle
GO:0051128	0.50	regulation of cellular component organization
GO:0045595	0.50	regulation of cell differentiation
GO:0010629	0.50	negative regulation of gene expression
GO:0009605	0.50	response to external stimulus
GO:0007154	0.50	cell communication

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:0044428	1.00	nuclear part
GO:0043226	0.78	organelle
GO:0043229	0.77	intracellular organelle
GO:0043231	0.76	intracellular membrane-bounded organelle
GO:0005634	0.73	nucleus
GO:0032991	0.72	macromolecular complex
GO:0043234	0.71	protein complex
GO:1902494	0.68	catalytic complex
GO:0044451	0.68	nucleoplasm part
GO:0035097	0.67	histone methyltransferase complex
GO:0005737	0.67	cytoplasm
GO:0044444	0.51	cytoplasmic part

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	1hbmA	0.453	4.29	0.047	0.760	2.8.4.1	96
2	0.060	1ug9A	0.417	4.08	0.040	0.702	3.2.1.70	NA
3	0.060	1mroB	0.447	4.09	0.070	0.721	2.8.4.1	NA
4	0.060	1r9jB	0.460	4.10	0.046	0.750	2.2.1.1	NA
5	0.060	1jqkF	0.439	4.01	0.068	0.712	1.2.99.2	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:

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	2aduA	0.456	4.06	0.051	0.788	0.12	R20	complex1.pdb.gz	53,92,103
2	0.01	2oazA	0.452	4.05	0.051	0.788	0.14	I96	complex2.pdb.gz	52,53,62,75,94
3	0.01	1r5gA	0.457	4.06	0.051	0.788	0.14	AO1	complex3.pdb.gz	4,5,22,23,64
4	0.01	1r5hA	0.457	4.05	0.051	0.788	0.13	AO2	complex4.pdb.gz	51,52,53,62,75
5	0.01	3fmqA	0.460	4.13	0.062	0.798	0.14	FUG	complex5.pdb.gz	40,73,91
6	0.01	2ea4A	0.457	4.05	0.051	0.788	0.12	F79	complex6.pdb.gz	37,85,87
7	0.01	3p9eh	0.463	4.21	0.036	0.760	0.12	UUU	complex7.pdb.gz	6,7,8,25,26,27,28

	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.