D-I-TASSER O15195-D4

D-I-TASSER results for O15195-D4

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

Input Sequence in FASTA format

>O15195 (149 residues)
EKRRRNQKLGGRDKSIHVKLDVGKLHTQPKLPSNKRLPEEVPSFQPRLFECSSHMGCLVL
AEVGFFSQEDLDKYDIMLLDTWQEIFLWLGEAASEWKEAVAWGQEYLKTHPAGRSPATPI
VLVKQGHEPPTFIGWFFTWDPYKWTSHPS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| EKRRRNQKLGGRDKSIHVKLDVGKLHTQPKLPSNKRLPEEVPSFQPRLFECSSHMGCLVLAEVGFFSQEDLDKYDIMLLDTWQEIFLWLGEAASEWKEAVAWGQEYLKTHPAGRSPATPIVLVKQGHEPPTFIGWFFTWDPYKWTSHPS
Prediction	CHHHHHHHHCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCSSSSSSCCCCHHHCCCCCSSSSSCCCSSSSSSCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCSSSSSCCCCCHHHHHHCCCCCCHHHCCCCC
Confidence	82466676367651267753212358877788643234555568983799984997599999437776558989779996698799997899978999999999999965048998983899928999989961236888023134799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| EKRRRNQKLGGRDKSIHVKLDVGKLHTQPKLPSNKRLPEEVPSFQPRLFECSSHMGCLVLAEVGFFSQEDLDKYDIMLLDTWQEIFLWLGEAASEWKEAVAWGQEYLKTHPAGRSPATPIVLVKQGHEPPTFIGWFFTWDPYKWTSHPS
Prediction	86544666355554314133424414335614665415763772422002023651403043126044630455100001034300002166164343015103300432466354512021034451153035204513553376568
	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                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHCCCCCSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCSSSSSSCCCCHHHCCCCCSSSSSCCCSSSSSSCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCSSSSSCCCCCHHHHHHCCCCCCHHHCCCCC
EKRRRNQKLGGRDKSIHVKLDVGKLHTQPKLPSNKRLPEEVPSFQPRLFECSSHMGCLVLAEVGFFSQEDLDKYDIMLLDTWQEIFLWLGEAASEWKEAVAWGQEYLKTHPAGRSPATPIVLVKQGHEPPTFIGWFFTWDPYKWTSHPS

1d0nA

0.40

0.34

10.09

1.17

DEthreader

--------------------AAILTADPVQSPAHLMASSLKKMHPPRLFACSNKIGRFVIEEVPGFMQEDLATDDVMLLDTWDQVFVWVGKDSQEKTEALTSAKRYIDTDPAHRDRRTPITVVKQGFEPPSFVGWFLGWDDSYWSVD--

1d0nA

0.37

0.36

10.57

2.36

SPARKS-K

RAQPVQVAEGSEPD-----SFWEALGGKATYRTSPRLKDKKMAHPPRLFACSNKIGRFVIEEPGEFMQEDLATDDVMLLDTWDQVFVWVGKDSQDEEKALTSAKRYIDTDPAHRDRRTPITVVKQGFEPPSFVGWFLGWDDSYWSVDPL

5a1kA

0.23

0.19

6.11

0.95

MapAlign

-------VEEGSEPSELIKVLGEKPELPDGGDDDDIIADISNRKMAKLYMVSD---SMRVTVVANFSMAMLLSEECFILDHGKQIFVWKGKDANPERKAMKTAEEFLQQ--MNYSKNTQIQVLPEGGETPIFKQFFKDWR---------

3ffkA

0.21

0.19

6.19

0.75

CEthreader

RARVHVSEEGTEPEAML--QVLGPKPALPAGTEDTAKEDAANRKLAKLYKVSNGAGTMSVSLVAPFAQGALKSEDCFILDHGKKIFVWKGKQANERKAALKTASDFITKM--DYPKQTQVSVLPEGGETPLFKQFFKNWRDPDQ-----

3fg7A

0.55

0.38

11.03

1.99

MUSTER

----------------------------------------NLVITPRLFECSNKTGRFLATEIPDFNQDDLEEDDVFLLDVWDQVFFWIGKHANEKKAAATTAQEYLKTHPSGRDPETPIIVVKQGHEPPTFTGWFLAWDPFKW-----

1d0nA

0.39

0.38

11.11

2.75

HHsearch

RAQPVQVAEGSEPDSF-----WEALGGKATYRTSPRLKDKMDAHPPRLFACSNKIGRFVIEEPGEFMQEDLATDDVMLLDTWDQVFVWVGKDSQDEKEALTSAKRYIDTDPAHRDRRTPITVVKQGFEPPSFVGWFLGWDDSYWSVDPL

3fg7A

0.54

0.38

10.85

1.65

FFAS-3D

----------------------------------------NLVITPRLFECSNKTGRFLATEIPDFNQDDLEEDDVFLLDVWDQVFFWIGKHANEEEKAATTAQEYLKTHPSGRDPETPIIVVKQGHEPPTFTGWFLAWDPFKW-----

1d0nA

0.34

10.03

1.42

EigenThreader

DAFVLKTPSAAYPDSFWEALGG----KATYRTSPRLKDKKMDAHPPRLFACSNKIGRFVIEEVPGEMQEDLATDDVMLLDTWDQVFVWVGKDSQDEEKTLTSAKRYIDTDPAHRDRRTPITVVKQGFEPPSFVGWFLGWDDSYWSVDPL

3ffnA

0.38

0.36

10.74

2.12

CNFpred

--QPVQVAEGSEP-----DGFWEALGGKAAYRTSPRLKDKKMAHPPRLFACSNKIGRFVIEEVPELMQEDLATDDVMLLDTWDQVFVWVGKDSQEKTEALTSAKRYIETDPANRDRRTPITVVKQGFEPPSFVGWFLGWDDDYWSVDPL

5a1kA

0.24

0.19

6.07

1.17

DEthreader

-------------YH--FELAIFTVMDPQNSDFVSRIIADISRKMAKLYMVSD---SMRVTVVEEFSMAMLLSEECFILDHAKQIFVWKGKDAPERKAAMKTAEEFLQQMN--YSKNTQIQVLPEGGETPIFKQFFKDWRD--------

(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	0.7691

(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	1d0nA	0.69	3.81	0.197	0.913	model1_1d0nA.pdb.gz
2	5a1kA	0.68	3.69	0.206	0.879	model1_5a1kA.pdb.gz
3	3fg6H	0.65	2.64	0.368	0.758	model1_3fg6H.pdb.gz
4	3fg7A	0.63	1.48	0.544	0.691	model1_3fg7A.pdb.gz
5	3ffkA3	0.60	2.36	0.231	0.685	model1_3ffkA3.pdb.gz
6	1j72A	0.58	2.01	0.123	0.664	model1_1j72A.pdb.gz
7	3eh1A	0.57	4.03	0.081	0.785	model1_3eh1A.pdb.gz
8	4pkiG1	0.55	2.45	0.150	0.638	model1_4pkiG1.pdb.gz
9	2vilA	0.50	2.94	0.160	0.631	model1_2vilA.pdb.gz
10	1ytuB2	0.40	4.84	0.054	0.658	model1_1ytuB2.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:0003779	0.89	actin binding
GO:0005509	0.64	calcium ion binding
GO:0032403	0.56	protein complex binding
GO:0051015	0.55	actin filament binding
GO:0005546	0.51	phosphatidylinositol-4,5-bisphosphate 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	0.97	single-organism process
GO:0009987	0.95	cellular process
GO:0044763	0.93	single-organism cellular process
GO:0016043	0.92	cellular component organization
GO:0030029	0.87	actin filament-based process
GO:0051014	0.85	actin filament severing
GO:0050794	0.79	regulation of cellular process
GO:0051128	0.76	regulation of cellular component organization
GO:0048522	0.73	positive regulation of cellular process
GO:0048523	0.72	negative regulation of cellular process
GO:0030833	0.72	regulation of actin filament polymerization
GO:0051693	0.71	actin filament capping
GO:0007015	0.68	actin filament organization
GO:0051130	0.64	positive regulation of cellular component organization
GO:0022607	0.62	cellular component assembly
GO:0050793	0.61	regulation of developmental process
GO:0051495	0.59	positive regulation of cytoskeleton organization
GO:0051239	0.59	regulation of multicellular organismal process
GO:0051240	0.57	positive regulation of multicellular organismal process
GO:0051125	0.57	regulation of actin nucleation
GO:0051016	0.56	barbed-end actin filament capping
GO:0032502	0.56	developmental process
GO:1902578	0.55	single-organism localization
GO:0050896	0.55	response to stimulus
GO:0044767	0.55	single-organism developmental process
GO:0032879	0.54	regulation of localization
GO:0044089	0.52	positive regulation of cellular component biogenesis
GO:0032268	0.52	regulation of cellular protein metabolic process
GO:0030162	0.52	regulation of proteolysis
GO:0030334	0.51	regulation of cell migration
GO:0022603	0.51	regulation of anatomical structure morphogenesis
GO:0009605	0.51	response to external stimulus
GO:0070887	0.50	cellular response to chemical stimulus
GO:0051127	0.50	positive regulation of actin nucleation
GO:0042989	0.50	sequestering of actin monomers
GO:0010033	0.50	response to organic substance
GO:0009719	0.50	response to endogenous stimulus
GO:0007165	0.50	signal transduction

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:0044424	1.00	intracellular part
GO:0043226	0.63	organelle
GO:0043229	0.55	intracellular organelle
GO:0005737	0.53	cytoplasm
GO:0044422	0.50	organelle 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	2w8nA	0.468	5.14	0.060	0.819	1.2.1.24	NA
2	0.060	3k2wB	0.487	5.29	0.074	0.873	1.2.1.8	NA
3	0.060	1bi9D	0.462	5.20	0.056	0.819	1.2.1.36 1.2.1.-	NA
4	0.060	3ifgA	0.473	5.29	0.059	0.839	1.2.1.16	NA
5	0.060	2wghB	0.449	4.14	0.056	0.671	1.17.4.1	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	0.04	1d0n0	0.688	3.81	0.197	0.913	0.50	III	complex1.pdb.gz	66,67,131,134,135
2	0.03	3cjbG	0.547	2.45	0.150	0.638	0.74	CA	complex2.pdb.gz	74,75,94,95
3	0.01	2bjaA	0.483	5.36	0.065	0.859	0.50	NAD	complex3.pdb.gz	88,90,91,126,127,129

	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.