D-I-TASSER Q17R55-D1

D-I-TASSER results for Q17R55-D1

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

Input Sequence in FASTA format

>Q17R55 (112 residues)
MPPMLWLLLHFAAPALGFYFSISCPSGKQCQQALLSGNDILLYCNSSGAHWYYLFTQGKK
GRLTSLTNISNMEIMPEGSLLIKDPLPSQTGLYHCWNKNGRQVVQYEIDFQD

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MPPMLWLLLHFAAPALGFYFSISCPSGKQCQQALLSGNDILLYCNSSGAHWYYLFTQGKKGRLTSLTNISNMEIMPEGSLLIKDPLPSQTGLYHCWNKNGRQVVQYEIDFQD
Prediction	CCHHHHHHHHHHHCCCCCCSSSSCCCCCHHHHHHCCCCCSSSSCCCCCCSSSSSCCCCCCCCCCCCCCCCCCSSCCCCCSSSCCCCCCCCCSSSSSCCCCCSSSSSSSSCCC
Confidence	9038999998542003653124458977344320059968996899995278852566555556644475513468995466388876673389862897289999841279
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MPPMLWLLLHFAAPALGFYFSISCPSGKQCQQALLSGNDILLYCNSSGAHWYYLFTQGKKGRLTSLTNISNMEIMPEGSLLIKDPLPSQTGLYHCWNKNGRQVVQYEIDFQD
Prediction	6423323332333233234330403565403301037340203054442302112244664423424425505334614130443346530203035754330141315258
	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                 100

                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHCCCCCCSSSSCCCCCHHHHHHCCCCCSSSSCCCCCCSSSSSCCCCCCCCCCCCCCCCCCSSCCCCCSSSCCCCCCCCCSSSSSCCCCCSSSSSSSSCCC
MPPMLWLLLHFAAPALGFYFSISCPSGKQCQQALLSGNDILLYCNSSGAHWYYLFTQGKKGRLTSLTNISNMEIMPEGSLLIKDPLPSQTGLYHCWNKNGRQVVQYEIDFQD

3dmkA

0.16

0.14

4.75

1.17

DEthreader

--------NKEVALVITEP-PKVVSLAKFDMKTYSGSSTMALLCPAQGYPVPVFRWYKFIKQAVV-LN-DRVKQV-SGTLIIKDAVVEDSGKYLCVVNNSVGGESVETVLTT

5o5gA4

0.17

0.14

4.68

1.10

SPARKS-K

--------------------EPPHFVVKPRDQVVALGRTVTFQCEATGNPQPAIFWRREGSNLLFSYSSSRFSVSQTGDLTITNVQRSDVGYYICQTLNVAGSIITKAYLEV

2id5B2

0.16

0.12

4.14

1.43

FFAS-3D

-------------------------DRKAQQVFVDEGHTVQFVCRADGDPPPAILWLSPRKHLVSAKSNGRLTVFPDGTLEVRYAQVQDNGTYLCIAANAGGNDSMPAHLH-

5k6uA

0.18

0.13

4.35

1.55

CNFpred

-----------------------------SRILGEVEETMDIPCRAMGVPLPTLQWYKDAVPLSKL-QNPRYKVLPSGGLHIQKLSPEDSGIFQCFASNEGGEVQTHTYLDV

1bihA

0.16

0.14

4.77

1.17

DEthreader

------AGDNLYFVDVVTGPVPQY---VSKDMMAKAGDVTMIYCMYGSNPMGYPNYFKN-GKDVNGNPEDRITHNTSGRLLFKTTLPEDEGVYTCEVDNGVKPQKHSLKLTV

5k6xA4

0.13

0.11

3.71

1.09

SPARKS-K

-------------------EPPQFVREPERHITAEMEKVVDIPCRAKGVPPPSITWYKDAALV-EVGKLTRFKQRSDGGLQISGLLPDDTGMLQCFAHNAAGEAQTSTYLAV

6xqqA

0.18

0.14

4.64

0.42

MapAlign

----------------------VEQ--NSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQSPELIMFKEDGRFTAQQYVSLLIRDSQPSDSATYLCAVRDGNMLTFGGTRLMV

6nrqA

0.15

0.12

4.22

0.34

CEthreader

----------------GSWNEPYFDLTMPRNITSLVGKSAYLGCRVKHLGNKTVAWIRHRDLHILTVGTQRFQTSDEWTLQIKWAQQRDAGVYECQISTQP-VRSYSVNLNI

2id5B

0.14

0.13

4.61

0.92

MUSTER

QGKEFKDFPDVLLPNYFTCRRARIRDRKAQQVFVDEGHTVQFVCRADGDPPPAILWLSPRKHLVSAKSNGRLTVFPDGTLEVRYAQVQDNGTYLCIAANAGGNDSMPAHLH-

6iaaA2

0.17

0.14

4.68

0.40

HHsearch

----------------APPQFV----VRPRDQIVAQGRTVTFPCETKGNPQPAVFWQKEGSQNLLFQPNSRCSVSPTGDLTITNIQRSDAGYYICQALTVAGSILAKAQVTD

(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	0.7766

(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	3dmkA	0.78	1.72	0.157	0.884	model1_3dmkA.pdb.gz
2	4cbpA	0.77	2.87	0.123	0.929	model1_4cbpA.pdb.gz
3	3lcyA	0.75	2.07	0.120	0.884	model1_3lcyA.pdb.gz
4	2edjA	0.75	1.87	0.200	0.848	model1_2edjA.pdb.gz
5	1bihA	0.75	2.69	0.145	0.920	model1_1bihA.pdb.gz
6	2nziA	0.75	2.03	0.120	0.866	model1_2nziA.pdb.gz
7	6efyA	0.75	2.40	0.128	0.884	model1_6efyA.pdb.gz
8	3lafA	0.75	2.36	0.131	0.884	model1_3lafA.pdb.gz
9	6iaaA	0.74	1.97	0.136	0.848	model1_6iaaA.pdb.gz
10	5k6xA	0.74	1.99	0.118	0.839	model1_5k6xA.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:0042802	0.65	identical protein binding
GO:0004872	0.61	receptor activity
GO:0004888	0.60	transmembrane signaling receptor activity
GO:0008046	0.54	axon guidance receptor activity
GO:0098632	0.51	protein binding involved in cell-cell adhesion
GO:0019904	0.51	protein domain specific 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	0.83	single-organism process
GO:0044763	0.77	single-organism cellular process
GO:0032502	0.72	developmental process
GO:0065007	0.71	biological regulation
GO:0044767	0.71	single-organism developmental process
GO:0050794	0.70	regulation of cellular process
GO:0051239	0.64	regulation of multicellular organismal process
GO:0050793	0.64	regulation of developmental process
GO:0016043	0.64	cellular component organization
GO:2000026	0.63	regulation of multicellular organismal development
GO:0006928	0.62	movement of cell or subcellular component
GO:0051128	0.59	regulation of cellular component organization
GO:0051960	0.58	regulation of nervous system development
GO:0048518	0.58	positive regulation of biological process
GO:0048869	0.57	cellular developmental process
GO:0048646	0.57	anatomical structure formation involved in morphogenesis
GO:0048523	0.57	negative regulation of cellular process
GO:0048522	0.57	positive regulation of cellular process
GO:0016477	0.57	cell migration
GO:0048583	0.56	regulation of response to stimulus
GO:0045595	0.56	regulation of cell differentiation
GO:0048856	0.55	anatomical structure development
GO:0010975	0.55	regulation of neuron projection development
GO:0048585	0.54	negative regulation of response to stimulus
GO:0009653	0.54	anatomical structure morphogenesis
GO:0007155	0.54	cell adhesion
GO:0001667	0.54	ameboidal-type cell migration
GO:0098609	0.53	cell-cell adhesion
GO:0051270	0.53	regulation of cellular component movement
GO:0040012	0.53	regulation of locomotion
GO:0032501	0.53	multicellular organismal process
GO:0030030	0.53	cell projection organization
GO:0060255	0.52	regulation of macromolecule metabolic process
GO:0051271	0.52	negative regulation of cellular component movement
GO:0044707	0.52	single-multicellular organism process
GO:0040013	0.52	negative regulation of locomotion
GO:0031323	0.52	regulation of cellular metabolic process
GO:0030334	0.52	regulation of cell migration
GO:0009966	0.52	regulation of signal transduction
GO:1902531	0.51	regulation of intracellular signal transduction
GO:0051961	0.51	negative regulation of nervous system development
GO:0048812	0.51	neuron projection morphogenesis
GO:0048584	0.51	positive regulation of response to stimulus
GO:0042981	0.51	regulation of apoptotic process
GO:0032268	0.51	regulation of cellular protein metabolic process
GO:0031325	0.51	positive regulation of cellular metabolic process
GO:0010604	0.51	positive regulation of macromolecule metabolic process
GO:0009968	0.51	negative regulation of signal transduction
GO:1902533	0.50	positive regulation of intracellular signal transduction
GO:0051129	0.50	negative regulation of cellular component organization
GO:0051056	0.50	regulation of small GTPase mediated signal transduction
GO:0050790	0.50	regulation of catalytic activity
GO:0048589	0.50	developmental growth
GO:0043065	0.50	positive regulation of apoptotic process
GO:0032270	0.50	positive regulation of cellular protein metabolic process
GO:0030162	0.50	regulation of proteolysis
GO:0022607	0.50	cellular component assembly
GO:0022603	0.50	regulation of anatomical structure morphogenesis
GO:0007166	0.50	cell surface receptor signaling pathway
GO:0002040	0.50	sprouting angiogenesis

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	0.95	cell part
GO:0044424	0.65	intracellular part
GO:0043226	0.63	organelle
GO:0016020	0.60	membrane
GO:0044444	0.57	cytoplasmic part
GO:0044425	0.51	membrane part
GO:0005737	0.51	cytoplasm
GO:0044422	0.50	organelle part
GO:0005886	0.50	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	0.175	2dm7A	0.639	2.56	0.125	0.786	2.7.11.1	58
2	0.120	2gqhA	0.616	2.23	0.102	0.741	2.7.11.1	63
3	0.117	2edtA	0.628	2.33	0.112	0.768	2.7.11.1	NA
4	0.074	2cknA	0.636	2.28	0.136	0.786	2.7.10.1	92
5	0.074	1tnnA	0.593	2.67	0.128	0.768	2.7.11.1	56,107

	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	0.08	1kcrL	0.676	2.28	0.132	0.812	0.87	III	complex1.pdb.gz	48,53,55,98,99,100,102
2	0.08	1cbvL	0.669	2.37	0.132	0.812	0.81	QNA	complex2.pdb.gz	48,49,53,99,100,101
3	0.03	1tlk0	0.731	1.92	0.104	0.830	0.95	III	complex3.pdb.gz	17,18,20,23,47,49,51,53,54,55,64,74,76
4	0.03	1kn4L	0.669	2.35	0.132	0.812	0.63	PDE	complex4.pdb.gz	21,23,46,48,51
5	0.03	1ejoL	0.678	2.28	0.121	0.812	0.63	III	complex5.pdb.gz	48,99,100,101,103

	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.