D-I-TASSER Q9UKR8-D2

D-I-TASSER results for Q9UKR8-D2

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

Input Sequence in FASTA format

>Q9UKR8 (79 residues)
FVTLRKNYRGYNEPDDYSTQWNLVMEKLKCCGVNNYTDFSGSSFEMTTGHTYPRSCCKSI
GSVSCDGRDVSPNVIHQKG

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| FVTLRKNYRGYNEPDDYSTQWNLVMEKLKCCGVNNYTDFSGSSFEMTTGHTYPRSCCKSIGSVSCDGRDVSPNVIHQKG
Prediction	CHCHHHHHHHCCCCHHHHHHHHHHHHCCSSSCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCC
Confidence	9118999972399835999999998007241218834347685425689918814157888888878768923422799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| FVTLRKNYRGYNEPDDYSTQWNLVMEKLKCCGVNNYTDFSGSSFEMTTGHTYPRSCCKSIGSVSCDGRDVSPNVIHQKG
Prediction	6431352166385574234212411442402314335114614244477441131034447564164454545523678
	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

                   |                   |                   |

SS
Seq

CHCHHHHHHHCCCCHHHHHHHHHHHHCCSSSCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCC
FVTLRKNYRGYNEPDDYSTQWNLVMEKLKCCGVNNYTDFSGSSFEMTTGHTYPRSCCKSIGSVSCDGRDVSPNVIHQKG

2m7zA

0.22

0.19

5.97

1.65

SPARKS-K

TSALKKLVDKYRNDEHVRKVFDEIQQKLHCCGADSPKDYGENP---------PTSCSKVQFTEGCIKKVSDLSKAH---

2m7zA

0.26

0.19

5.85

1.51

MUSTER

TSALKKLVDKYRNDEHVRKVFDEIQQKLHCCGADSPKDYGE---------NPPTSCSK-------------DGVQFTEG

1iv5A

0.14

0.11

3.87

1.97

HHsearch

KQFYDQALQQAVVDNNAKAVVKTFHETLDCCGSSTLTALTT--------SVLKNNLCPSG-S--N-----IISNLFKED

3kuqA

0.09

0.08

2.89

1.00

DEthreader

LQSIQQAMRLRHCAYDVADMLKQYFRDLPLM-ENRLQTLLYF-LSDVTAPLALASLFHLNDEAAGLAH-----------

6wvgA1

0.18

0.15

4.95

1.58

SPARKS-K

AKGLTDSIHRYHSDNSTKAAWDSIQSFLQCCGIAGTSDW---------TSGPPASCPSDRKVEGCYAKARLWFHSN---

6pbcA1

0.07

0.06

2.59

0.63

MapAlign

HSSEKWFHGKLGAGRDGRHIAERLLTEPDGSFL--------VRESETFVGDYTLSFWRNGKVQHCRIHSRFEMRLSEP-

2m7zA

0.19

0.16

5.32

0.87

CEthreader

TSALKKLVDKYRNDEHVRKVFDEIQQKLHCCGADSPKDYGEN---------PPTSCSKDGVQFTEGCIKKVSDLSKAH-

1iv5A

0.14

0.11

3.87

1.28

MUSTER

KQFYDQALQQAVVANNAKAVVKTFHETLDCCGSSTLTALTTSV--------LKNNLCPS--------GSNIISNLFKED

2m7zA

0.26

0.19

5.85

1.92

HHsearch

TSALKKLVDKYRNDEHVRKVFDEIQQKLHCCGADSPKDYGE---------NPPTSCSKD-------------GVQFTEG

6wvgA1

0.22

0.15

4.80

0.88

FFAS-3D

-KGLTDSIHRYHSDNSTKAAWDSIQSFLQCCGIAGTSDWTSG---------PPASCPSDRKVEGC--------------

(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	0.6952

(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	2m7zA	0.59	1.84	0.224	0.734	model1_2m7zA.pdb.gz
2	6wvgA1	0.57	1.83	0.196	0.709	model1_6wvgA1.pdb.gz
3	2qv2A2	0.55	3.52	0.041	0.873	model1_2qv2A2.pdb.gz
4	3cxlA	0.54	3.34	0.051	0.886	model1_3cxlA.pdb.gz
5	3gq2A3	0.54	3.45	0.029	0.823	model1_3gq2A3.pdb.gz
6	5tcxA	0.54	2.53	0.115	0.759	model1_5tcxA.pdb.gz
7	1iv5A	0.54	2.59	0.131	0.759	model1_1iv5A.pdb.gz
8	5oqrA	0.54	3.05	0.051	0.835	model1_5oqrA.pdb.gz
9	4gnsB	0.54	3.46	0.026	0.861	model1_4gnsB.pdb.gz
10	2bnxB	0.53	3.69	0.096	0.911	model1_2bnxB.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:0005215	0.44	transporter activity
GO:0022857	0.41	transmembrane transporter activity
GO:0022891	0.38	substrate-specific transmembrane transporter activity
GO:0004871	0.37	signal transducer activity
GO:0015075	0.31	ion transmembrane transporter activity
GO:0004872	0.30	receptor 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:0050794	1.00	regulation of cellular process
GO:0007166	0.99	cell surface receptor signaling pathway
GO:0044699	0.63	single-organism 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:0005887	1.00	integral component of 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

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	2gv9B	0.480	4.35	0.053	0.886	2.7.7.7	23,25
2	0.060	3ismC	0.481	4.10	0.028	0.823	3.6.1.3	42,53
3	0.060	3bc9A	0.483	3.84	0.069	0.810	3.2.1.1	NA
4	0.060	1ujkB	0.469	3.74	0.056	0.785	3.4.23.46	NA
5	0.060	1brwA	0.487	4.14	0.068	0.886	2.4.2.2	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	0.01	1u6hA	0.327	4.01	0.033	0.608	0.15	III	complex1.pdb.gz	17,20,21,24,31,32,66
2	0.01	3nzsA	0.464	4.14	0.067	0.835	0.15	NZS	complex2.pdb.gz	1,28,33,38
3	0.01	2bapA	0.470	3.71	0.039	0.823	0.10	III	complex3.pdb.gz	32,36,58
4	0.01	3r7qA	0.462	4.05	0.042	0.873	0.10	FAV	complex4.pdb.gz	21,29,30,31
5	0.01	3p2bA	0.524	3.31	0.070	0.810	0.12	P2B	complex5.pdb.gz	76,77,78,79
6	0.01	3s2aA	0.458	4.08	0.028	0.873	0.12	2NQ	complex6.pdb.gz	25,36,75
7	0.01	1xwjA	0.339	3.85	0.033	0.608	0.10	III	complex7.pdb.gz	16,19,20,32,33,36
8	0.01	3nzuA	0.522	3.28	0.070	0.810	0.16	NZU	complex8.pdb.gz	18,24,26,32,33
9	0.01	3tj5A	0.322	4.50	0.032	0.646	0.14	III	complex9.pdb.gz	14,15,18,21,22,24,25,28,29

	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.