D-I-TASSER Q9UPT6-D3

D-I-TASSER results for Q9UPT6-D3

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

Input Sequence in FASTA format

>Q9UPT6 (88 residues)
PPPAKRPYPSVNIHYKSPTTAGFSQRRNHAMCPISAGSRPLEFFPDDDCTSSARREQKRE
QYRQVREHVRNDDGRLQACGWSLPAKYK

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| PPPAKRPYPSVNIHYKSPTTAGFSQRRNHAMCPISAGSRPLEFFPDDDCTSSARREQKREQYRQVREHVRNDDGRLQACGWSLPAKYK
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCSSSSSCCCCCCCC
Confidence	9855589999865467998888754457654431136664556677764127898999999999999851146763676225775679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| PPPAKRPYPSVNIHYKSPTTAGFSQRRNHAMCPISAGSRPLEFFPDDDCTSSARREQKREQYRQVREHVRNDDGRLQACGWSLPAKYK
Prediction	8656746544442425435554454554544454555444252255754446543653464254045205567342212113235638
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCSSSSSCCCCCCCC
PPPAKRPYPSVNIHYKSPTTAGFSQRRNHAMCPISAGSRPLEFFPDDDCTSSARREQKREQYRQVREHVRNDDGRLQACGWSLPAKYK

5u0hA3

0.08

3.15

0.48

CEthreader

ASVRASLTAYADELVRWASANGYRSVLRPTDYFWGSAREAMGRAQALLLADRAYLETALDQAHWLFGRNAAGTSFMTGIGMHSPQKPH

3j4aA

0.05

2.23

0.53

EigenThreader

MAEKRTGLAEDGNDRAPYETRAQNCAQYTIPSLFPKDSDDYQTPWQAVGARGLNNLASKLMLWMRLTISEYEAKQLLSDPDGLAKVDE

6rawA1

0.12

0.11

3.99

0.35

FFAS-3D

---SHRPLDVCNIYSDRQVCILGDASLEENIPAFESGAGESDQEDQAPHEQRILKQRARRQWESERDRIMFEYTQFSYYGRSAA----

3hgfC

0.09

0.08

3.02

0.81

SPARKS-K

--KKIENIVTKIDKKKYIYKKLLNEIAEIEKDKTSLGKSLNKLFLEKIKKKSENMIKSMEKYIKDLDEIKEQSPKAEMN---------

2p51A

0.19

0.06

1.84

0.59

CNFpred

----------------------------------------------------------DYHYQTLRANVDS---KIIQIGLALSDEEG

5wlcSB

0.06

0.05

2.01

0.83

DEthreader

------------TQTLDNALAEQIVEFAAYREQNSAMKPTGASLVGQATKNGKIARVLAAKAAVSLRYDALAEDRDDGD-GL------

6rflA5

0.10

3.75

0.87

MapAlign

GKDIYTYLIGEKINYPGLLKDGEIIANDVDSNFVVAMRHLSLAGLLSDHKSNVEGINFIIKSSYVFKMVVDGYGQVVIGNTLIKYAA-

5ttaA

0.15

4.99

0.61

MUSTER

GEVGSVGFSPAGVDYGIVTGISPVSPKSYSHTYRKQQSPPQDIISFEKQQGKAWVENWLKEWKQEKEYAKQNPGKNQNDAFLLFDKWK

3mfbA

0.16

0.08

2.65

0.75

HHsearch

------------------------------------------LLTPEKL--LEAANKQGTVPSRVRYQWEDETGRLKAVGYHTSESGR

3j4aA

0.05

2.23

0.48

CEthreader

AKSVYERLKNDRAPYETRAQNCAQYTIPSLFPKDSDNASTDYQTPWQAVGARGLNNLASKLMLTISEYEAKQLLSDPDGLAKVDEGLS

(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	0.4114

(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	5xe5A	0.53	3.64	0.051	0.830	model1_5xe5A.pdb.gz
2	1uw5A	0.53	4.00	0.077	0.875	model1_1uw5A.pdb.gz
3	1ithA	0.52	3.36	0.049	0.807	model1_1ithA.pdb.gz
4	2lghA	0.52	3.62	0.082	0.807	model1_2lghA.pdb.gz
5	6rkoB	0.52	3.84	0.048	0.830	model1_6rkoB.pdb.gz
6	2zqpY1	0.52	3.50	0.094	0.807	model1_2zqpY1.pdb.gz
7	4rbnA3	0.52	3.51	0.091	0.818	model1_4rbnA3.pdb.gz
8	3tgoC	0.51	3.84	0.082	0.830	model1_3tgoC.pdb.gz
9	2lcgA	0.50	3.82	0.026	0.807	model1_2lcgA.pdb.gz
10	3mp7A1	0.43	3.99	0.037	0.727	model1_3mp7A1.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:0019900	1.00	kinase binding
GO:0032947	0.97	protein complex scaffold
GO:0030159	0.95	receptor signaling complex scaffold activity
GO:0019901	0.94	protein kinase binding
GO:0019894	0.93	kinesin binding
GO:0005078	0.93	MAP-kinase scaffold activity
GO:0008432	0.90	JUN kinase 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	0.98	regulation of cellular process
GO:0006810	0.97	transport
GO:0009966	0.94	regulation of signal transduction
GO:0080090	0.93	regulation of primary metabolic process
GO:0060255	0.93	regulation of macromolecule metabolic process
GO:0031323	0.93	regulation of cellular metabolic process
GO:0046328	0.92	regulation of JNK cascade
GO:0048518	0.91	positive regulation of biological process
GO:0016192	0.91	vesicle-mediated transport
GO:0048522	0.90	positive regulation of cellular process
GO:0048584	0.87	positive regulation of response to stimulus
GO:0031325	0.86	positive regulation of cellular metabolic process
GO:0009967	0.86	positive regulation of signal transduction
GO:0043507	0.85	positive regulation of JUN kinase activity
GO:0007257	0.84	activation of JUN kinase 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 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	0.98	intracellular part
GO:0005737	0.91	cytoplasm

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	1qh4A	0.494	3.95	0.060	0.818	2.7.3.2	NA
2	0.060	2vycA	0.471	3.41	0.070	0.761	4.1.1.19	NA
3	0.060	2guwB	0.423	4.24	0.079	0.841	3.2.2.4	NA
4	0.060	2gl6A	0.471	4.11	0.074	0.784	2.7.3.2	NA
5	0.060	1ejiA	0.469	3.51	0.029	0.739	2.1.2.1	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	3lb2B	0.488	3.52	0.068	0.739	0.17	HEM	complex1.pdb.gz	23,65,66
2	0.01	1vrpB	0.490	3.48	0.048	0.784	0.10	ADP	complex2.pdb.gz	9,68,73,74
3	0.01	2qfkB	0.488	3.49	0.041	0.750	0.12	HEM	complex3.pdb.gz	28,29,76,77,79
4	0.01	1ew6A	0.490	3.52	0.041	0.750	0.10	HEM	complex4.pdb.gz	41,43,61
5	0.01	2qfnA	0.493	3.46	0.041	0.750	0.11	UUU	complex5.pdb.gz	33,36,74,77,80
6	0.01	3dr9B	0.437	3.76	0.083	0.716	0.18	HEM	complex6.pdb.gz	22,65,68
7	0.01	3b6rB	0.489	4.08	0.060	0.818	0.14	ADP	complex7.pdb.gz	69,70,79,80,81,82
8	0.01	3lb4B	0.510	3.45	0.066	0.773	0.10	HEM	complex8.pdb.gz	73,74,77
9	0.01	3drbB	0.488	4.12	0.048	0.818	0.10	ADP	complex9.pdb.gz	11,72,74,75,79,80
10	0.01	3o7nA	0.491	3.48	0.041	0.750	0.11	HEM	complex10.pdb.gz	34,82,83

	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.