D-I-TASSER O14713-D1

D-I-TASSER results for O14713-D1

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

Input Sequence in FASTA format

>O14713 (200 residues)
MFRKGKKRHSSSSSQSSEISTKSKSVDSSLGGLSRSSTVASLDTDSTKSSGQSNNNSDTC
AEFRIKYVGAIEKLKLSEGKGLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIK
VSTSDQYDVLHRHALYLIIRMVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQA
QAICKVLSTAFDSVLTSEKP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MFRKGKKRHSSSSSQSSEISTKSKSVDSSLGGLSRSSTVASLDTDSTKSSGQSNNNSDTCAEFRIKYVGAIEKLKLSEGKGLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIRMVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVLTSEKP
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCSSSSSSSSSSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCSSSSSSSSCSSSSSCCCCCCSSSSCCCSSSSSSSSSSCCCCCCCSSSSSSSSCCCCCSSSSSSSSCCCHHHHHHHHHHHHHHHHHHHCCCCC
Confidence	97655333466655567655554212100267566754446882342036777766651158998987335355555676532389999999999970888999987449999950228972488773255302212567778642766651699999623897608999998199899999999999999999703689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MFRKGKKRHSSSSSQSSEISTKSKSVDSSLGGLSRSSTVASLDTDSTKSSGQSNNNSDTCAEFRIKYVGAIEKLKLSEGKGLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIRMVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVLTSEKP
Prediction	73552454356554544645544552466346254443335254743554544644343314030301220372643545436433400420341443351333455230001023310201445653022320022003001222334423100002124454540100001034473044004103400410145668
	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                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCSSSSSSSSSSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCSSSSSSSSCSSSSSCCCCCCSSSSCCCSSSSSSSSSSCCCCCCCSSSSSSSSCCCCCSSSSSSSSCCCHHHHHHHHHHHHHHHHHHHCCCCC
MFRKGKKRHSSSSSQSSEISTKSKSVDSSLGGLSRSSTVASLDTDSTKSSGQSNNNSDTCAEFRIKYVGAIEKLKLSEGKGLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIRMVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVLTSEKP

6ituA

0.16

0.10

3.50

1.00

DEthreader

---------------------------------------HTP-E-----------LSKHFIPYNAKFLGSTEV-EQP-----KGTEVVRDAVRKLK--FARIK-QKIPKVELQISIYGVKILEPKTKEVQHNCQLHRISFCADDKT--D--KRIFTFICKDSESNKHLCYVFDSEK--CAEEITLTIGQAFDLAYRKFLE

4dx8A

0.99

0.69

19.19

2.14

SPARKS-K

------------------------------------------------------NNSDTCAEFRIKYVGAIEKLK---LSGLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIRMVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVLT----

4dx8A

0.99

0.68

18.91

0.92

MapAlign

--------------------------------------------------------SDTCAEFRIKYVGAIEKLKL---SGLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIRMVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVL-----

4dx8A

0.99

0.69

19.32

0.87

CEthreader

------------------------------------------------------NNSDTCAEFRIKYVGAIEKLKL---SGLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIRMVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVLT----

4dx8A

1.00

0.69

19.46

1.80

MUSTER

------------------------------------------------------NNSDTCAEFRIKYVGAIEKLKLS---GLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIRMVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVLT----

4dx8A

0.99

0.69

19.32

2.88

HHsearch

------------------------------------------------------NNSDTCAEFRIKYVGAIEKLKL---SGLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIRMVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVLT----

4dx8A

0.98

0.67

18.77

2.28

FFAS-3D

--------------------------------------------------------SDTCAEFRIKYVGAIEKL---KLSGLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIRMVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVLT----

4dx8A

1.00

0.69

19.46

0.92

EigenThreader

------------------------------------------------------NNSDTCAEFRIKYVGAIEKLKLS---GLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIRMVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVLT----

3so6A

0.17

0.11

3.63

1.72

CNFpred

---------------------------------------------------------MEGMVFSLKYLGMTLVERP------KGEELSAAAVKRIVATAKA-SGKKLQKVTLKVSPRGIILTDSLTSQLIENVSIYRISYCTADK----MHDKVFAYIAQSQQNESLECHAFLCTKRKVAQAVTLTVAQAFKVAFEFWQV

4dx8A

0.93

0.63

17.69

1.00

DEthreader

----------------------------N-------N---SD----------------TCAEFRIKYVGAIELKL--S--GLEGPLDLINYIDVAQQDGKLP-VPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIRMVCYDD-GLGGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVLT----

(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	0.7124

(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	4dx8A	0.65	1.67	0.957	0.695	model1_4dx8A.pdb.gz
2	4wj7A	0.60	1.85	0.241	0.665	model1_4wj7A.pdb.gz
3	6ituA	0.60	2.27	0.156	0.675	model1_6ituA.pdb.gz
4	3so6A	0.59	2.06	0.162	0.650	model1_3so6A.pdb.gz
5	1ntvA	0.59	3.02	0.115	0.695	model1_1ntvA.pdb.gz
6	1m7eA	0.58	2.85	0.109	0.685	model1_1m7eA.pdb.gz
7	1wj1A	0.57	2.63	0.101	0.680	model1_1wj1A.pdb.gz
8	3suzA	0.57	2.88	0.156	0.675	model1_3suzA.pdb.gz
9	3dxdA	0.57	2.09	0.094	0.635	model1_3dxdA.pdb.gz
10	2m38A	0.56	2.40	0.171	0.645	model1_2m38A.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:0032403	1.00	protein complex binding
GO:0008565	1.00	protein transporter activity
GO:0005092	1.00	GDP-dissociation inhibitor activity
GO:0005102	0.52	receptor binding
GO:0050839	0.51	cell adhesion molecule binding
GO:0005178	0.50	integrin 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:2001044	1.00	regulation of integrin-mediated signaling pathway
GO:1900025	1.00	negative regulation of substrate adhesion-dependent cell spreading
GO:0090315	1.00	negative regulation of protein targeting to membrane
GO:0090314	1.00	positive regulation of protein targeting to membrane
GO:0090051	1.00	negative regulation of cell migration involved in sprouting angiogenesis
GO:0070373	1.00	negative regulation of ERK1 and ERK2 cascade
GO:0051897	1.00	positive regulation of protein kinase B signaling
GO:0051895	1.00	negative regulation of focal adhesion assembly
GO:0051496	1.00	positive regulation of stress fiber assembly
GO:0051451	1.00	myoblast migration
GO:0050880	1.00	regulation of blood vessel size
GO:0045944	1.00	positive regulation of transcription from RNA polymerase II promoter
GO:0045747	1.00	positive regulation of Notch signaling pathway
GO:0044344	1.00	cellular response to fibroblast growth factor stimulus
GO:0043113	1.00	receptor clustering
GO:0043087	1.00	regulation of GTPase activity
GO:0035924	1.00	cellular response to vascular endothelial growth factor stimulus
GO:0035148	1.00	tube formation
GO:0033628	1.00	regulation of cell adhesion mediated by integrin
GO:0033622	1.00	integrin activation
GO:0032148	1.00	activation of protein kinase B activity
GO:0032091	1.00	negative regulation of protein binding
GO:0015031	1.00	protein transport
GO:0010764	1.00	negative regulation of fibroblast migration
GO:0010595	1.00	positive regulation of endothelial cell migration
GO:0008285	1.00	negative regulation of cell proliferation
GO:0008284	1.00	positive regulation of cell proliferation
GO:0007229	1.00	integrin-mediated signaling pathway
GO:0006933	1.00	negative regulation of cell adhesion involved in substrate-bound cell migration
GO:0006469	1.00	negative regulation of protein kinase activity
GO:0002043	1.00	blood vessel endothelial cell proliferation involved in sprouting angiogenesis
GO:0051894	0.75	positive regulation of focal adhesion assembly
GO:0007155	0.52	cell adhesion
GO:0007160	0.50	cell-matrix adhesion

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:0071944	1.00	cell periphery
GO:0048471	1.00	perinuclear region of cytoplasm
GO:0030027	1.00	lamellipodium
GO:0005925	1.00	focal adhesion
GO:0005886	1.00	plasma membrane
GO:0005856	1.00	cytoskeleton
GO:0005829	1.00	cytosol
GO:0005737	1.00	cytoplasm
GO:0005634	1.00	nucleus
GO:0001726	1.00	ruffle
GO:0044421	0.53	extracellular region part
GO:0070062	0.50	extracellular exosome

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	2yt2A	0.405	2.77	0.107	0.470	2.7.10.1	155
2	0.060	1rp5A	0.379	5.64	0.015	0.660	3.4.-.-	NA
3	0.060	1itwB	0.392	5.17	0.054	0.655	1.1.1.42	71
4	0.060	2vhwE	0.381	5.59	0.061	0.660	1.4.1.1	NA
5	0.060	3i12A	0.386	4.90	0.032	0.610	6.3.2.4	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	0.03	2d10A	0.478	3.64	0.118	0.600	0.64	III	complex1.pdb.gz	121,123,132,133,138,157,159,171,172
2	0.02	1m7eA	0.580	2.85	0.109	0.685	0.72	III	complex2.pdb.gz	135,136,137,138,139,140,141,167,184,187,188,191
3	0.02	2emtA	0.473	3.77	0.118	0.595	0.78	III	complex3.pdb.gz	181,184,188
4	0.02	2yvcC	0.469	3.67	0.112	0.585	0.69	III	complex4.pdb.gz	160,177,181,184,188

	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.