D-I-TASSER Q9UJ72-D1

D-I-TASSER results for Q9UJ72-D1

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

Input Sequence in FASTA format

>Q9UJ72 (88 residues)
MFCGDYVQGTIFPAPNFNPIMDAQMLGGALQGFDCDKDMLINILTQRCNAQRMMIAEAYQ
SMYGRDLIGDMREQLSDHFKDVMAGLMY

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MFCGDYVQGTIFPAPNFNPIMDAQMLGGALQGFDCDKDMLINILTQRCNAQRMMIAEAYQSMYGRDLIGDMREQLSDHFKDVMAGLMY
Prediction	CCCCCCCCCCSSCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHC
Confidence	9999875454316999998999999999981579967999999965999999999999999979868999998668259999999719
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MFCGDYVQGTIFPAPNFNPIMDAQMLGGALQGFDCDKDMLINILTQRCNAQRMMIAEAYQSMYGRDLIGDMREQLSDHFKDVMAGLMY
Prediction	7364742402032466141640063025005434354410030015344620440263057427550263047403441340002115
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCSSCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHC
MFCGDYVQGTIFPAPNFNPIMDAQMLGGALQGFDCDKDMLINILTQRCNAQRMMIAEAYQSMYGRDLIGDMREQLSDHFKDVMAGLMY

4mduA

0.31

9.26

1.50

DEthreader

-HGKHYRP-TIKPTTGFSASADAERLHRSMKGPGTNELAIINILARRTNYERQEICQSYKSLYKQDLKDDLKSDTSGDFRKVLCQLIV

1dm5A2

0.33

0.31

9.23

2.26

SPARKS-K

-----VVQGTVKPHASFNSREDAETLRKAMKGIGTDEKSITHILATRSNAQRQQIKTDYTTLFGKHLEDELKSELSGNYEAAALALLR

1axnA2

0.41

0.36

10.70

0.84

MapAlign

----------VRDYPDFSPSVDAEAIQKAIRGIGTDEKMLISILTERSNAQRQLIVKEYQAAYGKELKDDLKGDLSGHFEHLMVALVT

1axnA2

0.39

11.43

0.57

CEthreader

ASIWVGHRGTVRDYPDFSPSVDAEAIQKAIRGIGTDEKMLISILTERSNAQRQLIVKEYQAAYGKELKDDLKGDLSGHFEHLMVALVT

1bc0A

0.37

0.35

10.45

1.41

MUSTER

-----ALRGTVTDFSGFDGRADAEVLRKAMKGLGTDEDSILNLLTARSNAQRQQIAEEFKTLFGRDLVNDMKSELTGKFEKLIVALMK

1dm5A

0.33

0.31

9.23

1.40

HHsearch

-----VVQGTVKPHASFNSREDAETLRKAMKGIGTDEKSITHILATRSNAQRQQIKTDYTTLFGKHLEDELKSELSGNYEAAALALLR

1xjlA1

0.33

0.31

9.22

1.49

FFAS-3D

-----SAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLL-

1hm6A

0.31

9.28

0.97

EigenThreader

KGSKGGPGSAVSPYPTFNPSSDVEALHKAITVKGVDEATIIEILTKRTNAQRQQIKAAYLQEKGKPLDEALKKALTGHLEEVALALLK

1bc0A

0.38

0.35

10.44

1.03

CNFpred

------LRGTVTDFSGFDGRADAEVLRKAMKGLGTDEDSILNLLTARSNAQRQQIAEEFKTLFGRDLVNDMKSELTGKFEKLIVALMK

1dm5A2

0.28

0.26

8.00

1.33

DEthreader

----VVQGTVKPHA-SFNSREDAETLRKAMKGIGTDEKSITHILATRSNAQRQQIKTDYTTLFGKHLEDELKSELSGNYEAAALALLR

(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

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.7765

(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

/jmol//j2s/core/package.js

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/jmol//j2s/core/core.z.js

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FileManager.getAtomSetCollectionFromFile(model1_1axnA2.pdb.gz)

FileManager opening 1 https://zhanglab.comp.nus.edu.sg/HPmod/data/Q9UJ72/Q9UJ72-D1/model1_1axnA2.pdb.gz

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The Resolver thinks Pdb

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Time for openFile(model1_1axnA2.pdb.gz): 2058 ms

reading 2649 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

2649 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.2.13_2015.03.07 2015-03-07 10:45 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,

and we thank the CMBI for maintaining it to the extent that it was easy to

re-engineer for our purposes. At this point in time, we make no guarantee

that this code gives precisely the same analysis as the code available via license

from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1axnA2	0.90	1.48	0.386	0.955	model1_1axnA2.pdb.gz
2	1dm5A2	0.89	0.88	0.313	0.920	model1_1dm5A2.pdb.gz
3	1bc0A	0.89	0.90	0.373	0.920	model1_1bc0A.pdb.gz
4	6tu2A1	0.89	0.94	0.383	0.920	model1_6tu2A1.pdb.gz
5	1m9iA	0.88	0.95	0.352	0.920	model1_1m9iA.pdb.gz
6	1xjlA1	0.88	1.31	0.321	0.932	model1_1xjlA1.pdb.gz
7	2zhjA	0.88	0.96	0.405	0.920	model1_2zhjA.pdb.gz
8	1hm6A	0.87	1.15	0.307	0.920	model1_1hm6A.pdb.gz
9	4mduA	0.87	1.61	0.295	0.943	model1_4mduA.pdb.gz
10	1w45A3	0.85	2.05	0.318	0.966	model1_1w45A3.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:0005543	0.64	phospholipid binding
GO:0046872	0.56	metal ion binding
GO:0005544	0.52	calcium-dependent phospholipid 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	0.94	single-organism process
GO:0009987	0.92	cellular process
GO:0044763	0.86	single-organism cellular process
GO:0065007	0.81	biological regulation
GO:0050789	0.79	regulation of biological process
GO:0050794	0.78	regulation of cellular process
GO:0006810	0.78	transport
GO:0044765	0.74	single-organism transport
GO:0016043	0.74	cellular component organization
GO:0050896	0.69	response to stimulus
GO:0006811	0.65	ion transport
GO:0055085	0.64	transmembrane transport
GO:0048519	0.64	negative regulation of biological process
GO:0042221	0.64	response to chemical
GO:0032879	0.64	regulation of localization
GO:0070588	0.63	calcium ion transmembrane transport
GO:0048523	0.62	negative regulation of cellular process
GO:0065008	0.61	regulation of biological quality
GO:0051239	0.61	regulation of multicellular organismal process
GO:0048522	0.61	positive regulation of cellular process
GO:0048583	0.60	regulation of response to stimulus
GO:0010033	0.59	response to organic substance
GO:2000145	0.58	regulation of cell motility
GO:0051049	0.58	regulation of transport
GO:0051241	0.57	negative regulation of multicellular organismal process
GO:0051051	0.57	negative regulation of transport
GO:0032101	0.57	regulation of response to external stimulus
GO:0023051	0.57	regulation of signaling
GO:0010646	0.57	regulation of cell communication
GO:0080134	0.56	regulation of response to stress
GO:0051716	0.56	cellular response to stimulus
GO:0009725	0.56	response to hormone
GO:1903531	0.55	negative regulation of secretion by cell
GO:0071495	0.54	cellular response to endogenous stimulus
GO:0071310	0.54	cellular response to organic substance
GO:0061041	0.54	regulation of wound healing
GO:0048585	0.54	negative regulation of response to stimulus
GO:0046883	0.53	regulation of hormone secretion
GO:0032870	0.53	cellular response to hormone stimulus
GO:0010035	0.53	response to inorganic substance
GO:1901700	0.52	response to oxygen-containing compound
GO:0065009	0.51	regulation of molecular function
GO:0051224	0.50	negative regulation of protein transport
GO:0042981	0.50	regulation of apoptotic process
GO:0022607	0.50	cellular component assembly

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	0.98	cell part
GO:0044424	0.94	intracellular part
GO:0043226	0.87	organelle
GO:0043227	0.79	membrane-bounded organelle
GO:0016020	0.77	membrane
GO:0044444	0.76	cytoplasmic part
GO:0044422	0.73	organelle part
GO:0044446	0.68	intracellular organelle part
GO:0031982	0.66	vesicle
GO:0043229	0.63	intracellular organelle
GO:0044421	0.62	extracellular region part
GO:0005737	0.61	cytoplasm
GO:0031988	0.60	membrane-bounded vesicle
GO:0043230	0.55	extracellular organelle
GO:0043231	0.54	intracellular membrane-bounded organelle
GO:0070062	0.53	extracellular exosome
GO:0031090	0.53	organelle membrane
GO:0005886	0.52	plasma membrane

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

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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	2vvnA	0.469	3.73	0.062	0.784	3.2.1.52	NA
2	0.060	2cw7A	0.504	3.78	0.086	0.886	2.7.7.7	NA
3	0.060	2gtqA	0.493	3.76	0.039	0.807	3.4.11.2	NA
4	0.060	1hn0A	0.577	3.57	0.071	0.909	4.2.2.20	65
5	0.060	1l2aE	0.470	3.88	0.000	0.841	3.2.1.4	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

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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	0.78	1annA	0.876	1.00	0.420	0.920	0.93	CA	complex1.pdb.gz	30,32,34
	2	0.57	1g5nA	0.890	0.91	0.373	0.920	1.52	UUU	complex2.pdb.gz	27,31,32,33,65,72,73

	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.