D-I-TASSER O60813-D2

D-I-TASSER results for O60813-D2

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

Input Sequence in FASTA format

>O60813 (121 residues)
PFRRLPLRPLIKMPCLEAFQAVLDGLDALLTQGVRPRRWKLQVLDLQDVCENFWMVWSEA
MAHGCFLNAKRNKKPVQDCPRMRGRQPLTVFVELWLKNRTLDEYLTCLLLWVKQRRDLLH
L

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| PFRRLPLRPLIKMPCLEAFQAVLDGLDALLTQGVRPRRWKLQVLDLQDVCENFWMVWSEAMAHGCFLNAKRNKKPVQDCPRMRGRQPLTVFVELWLKNRTLDEYLTCLLLWVKQRRDLLHL
Prediction	CCCCCCHHHHCCCCCHHHHHHHHHCHHHHHCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCSSSSSSSSSCCCCCCHHHHHHHHHHHHHCCCCCC
Confidence	9887770453267767999999834243321566777665426542226765356367865678562122034432348764466567999986735786676899999999962255569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| PFRRLPLRPLIKMPCLEAFQAVLDGLDALLTQGVRPRRWKLQVLDLQDVCENFWMVWSEAMAHGCFLNAKRNKKPVQDCPRMRGRQPLTVFVELWLKNRTLDEYLTCLLLWVKQRRDLLHL
Prediction	8243030120264433410300143142233452444434041030342446224133444444224533455543763654544330301010103463244103100510552453347
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCHHHHCCCCCHHHHHHHHHCHHHHHCCCCCCCCCCCSSSSSSCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCSSSSSSSSSCCCCCCHHHHHHHHHHHHHCCCCCC
PFRRLPLRPLIKMPCLEAFQAVLDGLDALLTQGVRPRRWKLQVLDLQDVCENFWMVWSEAMAHGCFLNAKRNKKPVQDCPRMRGRQPLTVFVELWLKNRTLDEYLTCLLLWVKQRRDLLHL

6hrhB

0.11

3.89

0.54

CEthreader

VELEQELAELHQKDSALLFSSCFVANDSTLF-TLAKILPGCEIYSDAGNHASMIQGIRNSGAAKFVFRHNDPDHLKKLLEKSNPKIPKIVAFETVHSMDGAICPLEELCDVSHQYGALTFV

3nzqA1

0.04

2.04

0.58

EigenThreader

GYNGDYFLVIKVNQHRRVIESLIHEIAIVLDEAERLNVVPRLGVRARLKWQSSSKFGLAATQVLQLVETLREAGR---------LDSLQLLHFHLGSQMANIRDIARFYVELHKLGVNIQC

4bbyA2

0.10

0.07

2.46

0.42

FFAS-3D

------------------FEQGVACLREIAKQRCAPA--SIRLMD---------------NQQFQFGHALKPQVSSIFTSGFDPNQLSVATLLFEGDREKVLQHEKQVYDIAAKFGG----

4wkkA3

0.13

0.12

4.04

0.71

SPARKS-K

ELTSLAKYLNSAPSLEDALFRTAQLVSSISGHD--------RTLIYDFGLDWSGHVVAEAGSGA-LPSYLGLRFPAGDIPPTINRLSIVVWGLIACHHATPHEACDFAAQLLSMRIAMEQ-

3o7wA

0.19

0.12

3.74

0.60

CNFpred

----------------RGYFARVHGVSQLIKAFLRKTECHCQIVNLGGMDTTFWRLKDE-------------------------DLLPSKYFEVDFP-----MIVTRKLHSIKCKPPLSSP

6tjvF

0.09

3.43

0.83

DEthreader

RVVAALVTLVALTALLVIGSVTALGGTLIAAQDIKRALSLVAYWVIAGLKEPGLAFVFI--LTYSLAMAVLMSISINSVTQDLRLLF-SGLLPQELTAAQLPWVGGVLLLMNTFAAFSLGA

7bwgA2

0.03

1.87

0.74

MapAlign

-SDDQGWRIELHSRPELTKDDYREIVEYAASRHMIV--VPEIDMPSHTHAIGLAEVGFSSLKIHDEATYDFAADVFGELAGMTPGPYLHLGGDEATAEEDFALFVSRVSTIIADLGKTPVA

5mx0A2

0.15

0.13

4.43

0.54

MUSTER

NVYTVPDSYFRGAPKLLYV---LSH-NNGLASNTF-NSSSLLELDLSYNQQKIPPVNTNLENNEFSISSFCTVVDVVNFSK------LQ-VLRLDIKRSAMPADAPLCLR-----ASLIEI

1vt4I

0.13

0.12

4.30

0.63

HHsearch

LKNCNSPETVLESDHSSNIKLRIHSIQAELRRLLSKPYENCLLVLLNVQNAKAWNAFN---LSCKILLTTRFKQV-TD--FLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR

4k1rA

0.03

1.88

0.52

CEthreader

--TFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAI

(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	0.5649

(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	3vvnA	0.52	4.32	0.078	0.934	model1_3vvnA.pdb.gz
2	4lz6A	0.52	4.35	0.043	0.909	model1_4lz6A.pdb.gz
3	4ix3A2	0.51	4.52	0.054	0.884	model1_4ix3A2.pdb.gz
4	6ei3A	0.51	4.28	0.050	0.843	model1_6ei3A.pdb.gz
5	4z3nA	0.47	4.86	0.071	0.926	model1_4z3nA.pdb.gz
6	1aq1A	0.47	4.51	0.089	0.802	model1_1aq1A.pdb.gz
7	1f0qA	0.47	4.19	0.054	0.777	model1_1f0qA.pdb.gz
8	1tkiA2	0.47	4.47	0.050	0.793	model1_1tkiA2.pdb.gz
9	1cm8A	0.46	4.72	0.040	0.810	model1_1cm8A.pdb.gz
10	1blxA	0.46	4.66	0.078	0.810	model1_1blxA.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:0042974	0.90	retinoic acid receptor binding
GO:1901363	0.56	heterocyclic compound binding
GO:0097159	0.56	organic cyclic compound 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:0080090	1.00	regulation of primary metabolic process
GO:0060255	1.00	regulation of macromolecule metabolic process
GO:0031323	1.00	regulation of cellular metabolic process
GO:0009966	1.00	regulation of signal transduction
GO:0044699	0.67	single-organism process
GO:0001932	0.63	regulation of protein phosphorylation
GO:0070372	0.58	regulation of ERK1 and ERK2 cascade
GO:0019827	0.58	stem cell population maintenance
GO:0009987	0.58	cellular 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:0043231	1.00	intracellular membrane-bounded organelle
GO:0005737	1.00	cytoplasm
GO:0044444	0.86	cytoplasmic part
GO:0005634	0.71	nucleus
GO:0044446	0.70	intracellular organelle part
GO:0032991	0.68	macromolecular complex
GO:0031982	0.56	vesicle
GO:0031988	0.55	membrane-bounded vesicle
GO:0001669	0.53	acrosomal vesicle

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	1bi9D	0.373	4.34	0.083	0.612	1.2.1.36 1.2.1.-	NA
2	0.060	1lufA	0.471	4.40	0.053	0.793	2.7.10.1	NA
3	0.060	1o9jA	0.464	4.68	0.066	0.818	1.2.1.3	NA
4	0.060	1vywA	0.457	4.76	0.079	0.810	2.7.11.22 2.7.1.37	NA
5	0.060	1e9yB	0.490	4.02	0.066	0.769	3.5.1.5	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	0.02	3dn2A	0.306	5.00	0.070	0.554	0.29	BBF	complex1.pdb.gz	26,29,30,33,42,43
2	0.01	183lA	0.304	4.83	0.070	0.537	0.29	DEN	complex2.pdb.gz	26,29,30
3	0.01	1owzA	0.297	4.58	0.047	0.512	0.19	4FA	complex3.pdb.gz	25,28,29,34
4	0.01	3htbA	0.317	4.34	0.000	0.529	0.29	JZ4	complex4.pdb.gz	26,34,41
5	0.01	2rbqA	0.298	4.67	0.036	0.521	0.24	263	complex5.pdb.gz	27,30,40
6	0.01	2rbnA	0.296	4.67	0.045	0.512	0.25	264	complex6.pdb.gz	26,34,41
7	0.01	3gulB	0.305	4.92	0.070	0.554	0.16	PYL	complex7.pdb.gz	25,30,36
8	0.01	1c6mA	0.298	4.82	0.045	0.521	0.23	KR	complex8.pdb.gz	1,2,23
9	0.01	1ovkA	0.300	4.79	0.070	0.529	0.20	NYL	complex9.pdb.gz	27,30,31,114,117,118
10	0.01	1c61A	0.298	4.58	0.047	0.512	0.36	KR	complex10.pdb.gz	22,23,26

	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.