D-I-TASSER Q9UF56-D3

D-I-TASSER results for Q9UF56-D3

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

Input Sequence in FASTA format

>Q9UF56 (155 residues)
LRHITELDNETVMEIVKRCKNLSSLNLCLNWIINDRCVEVIAKEGQNLKELYLVSCKITD
YALIAIGRYSMTIETVDVGWCKEITDQGATLIAQSSKSLRYLGLMRCDKVNEVTVEQLVQ
QYPHITFSTVLQDCKRTLERAYQMGWTPNMSAASS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| LRHITELDNETVMEIVKRCKNLSSLNLCLNWIINDRCVEVIAKEGQNLKELYLVSCKITDYALIAIGRYSMTIETVDVGWCKEITDQGATLIAQSSKSLRYLGLMRCDKVNEVTVEQLVQQYPHITFSTVLQDCKRTLERAYQMGWTPNMSAASS
Prediction	CCCCCCCCHHHHHHHHHHCCCCCSSSCCCCCCCCHHHHHHHHHHCCCCCSSSSSCCSCCHHHHHHHHHCCCCCCSSSCCCCCCCCHHHHHHHHHCCCCCCSSSCCCCCCCCHHHHHHHHHHCCCCSSSSSCCCCCCCCHHHHHHHHCCCCCCCCC
Confidence	95988688799999998099998898118999898999999981999978983187275899999997099998898359898588999999980999988983599993989999999818567567661689866779988762578886889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| LRHITELDNETVMEIVKRCKNLSSLNLCLNWIINDRCVEVIAKEGQNLKELYLVSCKITDYALIAIGRYSMTIETVDVGWCKEITDQGATLIAQSSKSLRYLGLMRCDKVNEVTVEQLVQQYPHITFSTVLQDCKRTLERAYQMGWTPNMSAASS
Prediction	85524522260133106405546442243044021400330054055144434540402150232004205524322443144311401320054055364544640433225034321641440322120440440134003212034254278
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCHHHHHHHHHHCCCCCSSSCCCCCCCCHHHHHHHHHHCCCCCSSSSSCCSCCHHHHHHHHHCCCCCCSSSCCCCCCCCHHHHHHHHHCCCCCCSSSCCCCCCCCHHHHHHHHHHCCCCSSSSSCCCCCCCCHHHHHHHHCCCCCCCCC
LRHITELDNETVMEIVKRCKNLSSLNLCLNWIINDRCVEVIAKEGQNLKELYLVSCKITDYALIAIGRYSMTIETVDVGWCKEITDQGATLIAQSSKSLRYLGLMRCDKVNEVTVEQLVQQYPHITFSTVLQDCKRTLERAYQMGWTPNMSAASS

6o60C

0.21

6.57

1.50

DEthreader

LSWCDQITKDGIEALVRGCRGLKALLLRGCTQLEDEALKHIQNYCHELVSLNLQSCRITDEGVVQICRGCHRLQALCLSGCSNLTDASLTALGLNCPRLQILEAARCSHLTDAGFTLLARNCHELEKM-DLEECILITDSTLILSICPKLQALSL

6o60C

0.22

6.92

1.51

SPARKS-K

LRGCIGVGDSSLKTFAQNCRNIEHLNLNGCTKITDSTCYSLSRFCSKLKHLDLTSCSITNSSLKGISEGCRNLEYLNLSWCDQITKDGIEALVRGCRGLKALLLRGCTQLEDEALKHIQNYCHELVS-LNLQSCSRITGVVQICRGCHRLQALCL

6o60C

0.20

0.19

6.01

0.76

MapAlign

LNGCTKITDSTCYSLSRFCSKLKHLDLTSCVSITNSSLKGISEGCRNLEYLNLSWCQITKDGIEALVRGCRGLKALLLRGCTQLEDEALKHIQNYCHELVSLNLQSCSRITDEGVVQICRGCHRLQAL-CLSGCSNLTDASLTALGLNC------

6o60C

0.19

6.22

0.57

CEthreader

LNGCTKITDSTCYSLSRFCSKLKHLDLTSCVSITNSSLKGISEGCRNLEYLNLSWCQITKDGIEALVRGCRGLKALLLRGCTQLEDEALKHIQNYCHELVSLNLQSCSRITDEGVVQICRGCHRLQAL-CLSGCSNLTDASLTALNCPRLQILEA

6o60C

0.21

6.57

1.39

MUSTER

LSWCDQITKDGIEALVRGCRGLKALLLRGCTQLEDEALKHIQNYCHELVSLNLQSCSITDEGVVQICRGCHRLQALCLSGCSNLTDASLTALGLNCPRLQILEAARCSHLTDAGFTLLARNCHELEKMD-LEECILITDSTLISIHCPKLQALSH

5zb2A3

0.13

4.46

0.95

HHsearch

ISNTHRFTDKSLSNLLINCSTLVSLGLSRLDSISNYALLPQYLVNDEFHSLCIEYPDVNDEIIINLGQIGRTLRKLVLNGCIDLTDSMIIGLTAFIPPLEVLSLEESDQITTDSLSYFFSKLNNLIEC-SFRRCLQLGDMAIILLNGASLRS---

6w66B

1.00

0.94

26.19

1.43

FFAS-3D

LRHITELDNETVMEIVKRCKNLSSLNLCLNWIINDRCVEVIAKEGQNLKELYLVSCKITDYALIAIGRYSMTIETVDVGWCKEITDQGATLIAQSSKSLRYLGLMRCDKVNEVTVEQLVQQYPHITFSTVLQDCKRTLERAYQMG----------

6o60C

0.19

6.05

0.65

EigenThreader

LNGCTKITDSTCYSLSRFCSKLKHLDLTSCVSITNSSLKGISEGCRNLEYLNLSWCQITKDGIEALVRGCRGLKALLLRGCTQLEDEALKHIQNYCHELVSLNLQSCSRITDEGVVQICRGCHRLQLCLSGCSNLTSLTALGLNCPRLQILEAAR

6w66B

1.00

0.95

26.55

2.23

CNFpred

LRHITELDNETVMEIVKRCKNLSSLNLCLNWIINDRCVEVIAKEGQNLKELYLVSCKITDYALIAIGRYSMTIETVDVGWCKEITDQGATLIAQSSKSLRYLGLMRCDKVNEVTVEQLVQQYPHITFSTVLQDCKRTLERAYQMGWT--------

6w66B

0.19

6.03

1.50

DEthreader

HVGNQDLTDEGLKQLGSKCRELKDIHFGQCYKISDEGMIVIAKGCLKLQRIYMQENKVTDQSVKAFAEHCPELQYVGFMGC-SVTSKGVIHLT-KLRNLSSLDLRHITELDNETVMEIVKRCKNLSSL-NLCLNWIINDRCVEIAKGQNLKELYV

(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	0.9144

(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	6o60C	0.96	0.88	0.208	0.994	model1_6o60C.pdb.gz
2	6w66B	0.93	1.07	0.184	0.981	model1_6w66B.pdb.gz
3	5zb2A	0.88	1.66	0.171	0.981	model1_5zb2A.pdb.gz
4	1k5gL	0.88	1.90	0.149	0.994	model1_1k5gL.pdb.gz
5	2assB	0.86	1.72	0.208	0.961	model1_2assB.pdb.gz
6	4perA	0.86	2.07	0.143	0.994	model1_4perA.pdb.gz
7	5jh5A	0.85	1.83	0.174	0.961	model1_5jh5A.pdb.gz
8	2p1oB2	0.85	1.89	0.134	0.961	model1_2p1oB2.pdb.gz
9	1dfjI3	0.84	2.11	0.144	0.987	model1_1dfjI3.pdb.gz
10	4xa9A	0.82	1.85	0.179	0.935	model1_4xa9A.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:1901363	0.60	heterocyclic compound binding
GO:0097159	0.60	organic cyclic compound binding
GO:0098772	0.56	molecular function regulator
GO:0030234	0.55	enzyme regulator activity
GO:0004857	0.54	enzyme inhibitor activity

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	0.90	cellular process
GO:0065007	0.82	biological regulation
GO:0050789	0.81	regulation of biological process
GO:0008152	0.73	metabolic process
GO:0071704	0.72	organic substance metabolic process
GO:0044238	0.72	primary metabolic process
GO:0044699	0.71	single-organism process
GO:0044237	0.70	cellular metabolic process
GO:0043170	0.70	macromolecule metabolic process
GO:0050794	0.69	regulation of cellular process
GO:0044260	0.69	cellular macromolecule metabolic process
GO:0032502	0.62	developmental process
GO:0044767	0.60	single-organism developmental process
GO:0065009	0.59	regulation of molecular function
GO:0044092	0.54	negative regulation of molecular function
GO:0051239	0.53	regulation of multicellular organismal process
GO:0050793	0.53	regulation of developmental process
GO:2000026	0.52	regulation of multicellular organismal development
GO:0048646	0.51	anatomical structure formation involved in morphogenesis
GO:0022603	0.50	regulation of anatomical structure morphogenesis

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:0044424	0.99	intracellular part
GO:0043226	0.89	organelle
GO:0043227	0.87	membrane-bounded organelle
GO:0043229	0.82	intracellular organelle
GO:0043231	0.79	intracellular membrane-bounded organelle
GO:0005634	0.75	nucleus
GO:0005737	0.71	cytoplasm
GO:0032991	0.70	macromolecular complex
GO:0043234	0.67	protein complex
GO:0044422	0.57	organelle part
GO:0044446	0.56	intracellular organelle part
GO:0044444	0.50	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	1itqA	0.551	4.46	0.076	0.877	3.4.13.19	NA
2	0.060	2o1dA	0.555	4.54	0.117	0.916	4.2.2.2	NA
3	0.060	2ifgA	0.639	3.32	0.081	0.865	2.7.10.1	45,48,99
4	0.060	1airA	0.578	4.32	0.064	0.903	4.2.2.2	140
5	0.060	1pclA	0.568	4.52	0.110	0.910	4.2.2.2	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	0.17	3c6nB	0.814	2.31	0.166	0.974	0.87	2S8	complex1.pdb.gz	54,77,78,79,101,103,104,129,130,131
2	0.14	2p1pB	0.816	2.33	0.127	0.968	0.77	IAC	complex2.pdb.gz	26,27,28,52,53,77,78,79,104
3	0.03	3a79B	0.724	3.11	0.130	0.942	0.71	UUU	complex3.pdb.gz	21,23,46,48
4	0.03	3a7cA	0.735	3.28	0.113	0.974	0.72	PDK	complex4.pdb.gz	46,57,58,59,60,64,82,87,108

	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.