D-I-TASSER P60484-D2

D-I-TASSER results for P60484-D2

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

Input Sequence in FASTA format

>P60484 (212 residues)
ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCG
DIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADN
DKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSD
NEPDHYRYSDTTDSDPENEPFDEDQHTQITKV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHTQITKV
Prediction	CCSSSSSSSSCCCCCCCCSSSSSSSSSSCCSSSSSCCCSSSCCCCCSSSSSSCCCCSSSCCSSSSSSSCCCCCCCCCSSSSSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCHHHCCCCCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCC
Confidence	91677999954565469804589999968887871685210257737999827983350767999996799876542589999876663177544211134665666665443456777888669998166772131105556738934228999951677767776667888676667788765554334568864467776621022159
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHTQITKV
Prediction	73304304032020035430201010124534113264361464442020305320302440202011375534443200100000000334544444344454254545443535546742410102042630151241662440265030312044266547545455545445545574454454444444456436346554443476
	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 DeepPotential. 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

CCSSSSSSSSCCCCCCCCSSSSSSSSSSCCSSSSSCCCSSSCCCCCSSSSSSCCCCSSSCCSSSSSSSCCCCCCCCCSSSSSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCHHHCCCCCCCCCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCC
ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHTQITKV

1d5rA2

0.96

0.58

16.14

0.83

DEthreader

ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIP-----------------------------KE--YLVLTLTKNDLDKAN--KDKAYFSPNFKVKLYFTKTV----------------------------------------------------

1d5rA2

0.98

0.60

16.78

1.91

SPARKS-K

ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPKE-------------------------------YLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTV----------------------------------------------------

3n0aA

0.23

0.14

4.28

0.92

MapAlign

PLTIKSITVSPVPFFNRNGCRPYCDVLIGETKIYTTCMKEYRVQDGKIFIPL--SITVQGDVVVSMYHLRSAKVTNTQIFQLQFHTGFI-------------------------------PLDTTVLKFTKPELDACD---VPEKYPQLFQVTLDVELQPH---------------------------------------------------

1d5rA2

0.99

0.60

16.91

0.75

CEthreader

ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPK-------------------------------EYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTV----------------------------------------------------

1d5rA2

0.98

0.59

16.66

1.64

MUSTER

ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPKEY-------------------------------LVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTV----------------------------------------------------

1d5rA2

0.98

0.59

16.66

4.93

HHsearch

ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPKEY-------------------------------LVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTV----------------------------------------------------

1d5rA2

0.98

0.59

16.52

2.16

FFAS-3D

ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPKEY-------------------------------LVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKT-----------------------------------------------------

1d5rA2

0.97

0.58

16.26

0.90

EigenThreader

ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPRED--KFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPK-------------------------------EYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTV----------------------------------------------------

5bugA

0.99

0.63

17.71

3.15

CNFpred

ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEEDN------------------------DKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTV----------------------------------------------------

1d5rA

0.98

0.60

16.78

0.83

DEthreader

ALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIP-----------------------------KE--YLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTV----------------------------------------------------

(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	0.6719

(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 DeepPotential, 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	1d5rA	0.60	0.79	0.984	0.609	model1_1d5rA.pdb.gz
2	3n0aA1	0.55	2.38	0.221	0.609	model1_3n0aA1.pdb.gz
3	3aweA	0.51	2.68	0.211	0.580	model1_3aweA.pdb.gz
4	2hc1A	0.32	5.87	0.049	0.566	model1_2hc1A.pdb.gz
5	1larA2	0.32	5.66	0.025	0.566	model1_1larA2.pdb.gz
6	2b3oA2	0.31	6.02	0.062	0.552	model1_2b3oA2.pdb.gz
7	2b49A	0.31	5.94	0.077	0.542	model1_2b49A.pdb.gz
8	3i1cA	0.31	5.85	0.024	0.538	model1_3i1cA.pdb.gz
9	1jlnA	0.31	5.37	0.058	0.505	model1_1jlnA.pdb.gz
10	1g4uS2	0.29	6.04	0.026	0.519	model1_1g4uS2.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:0016791	1.00	phosphatase activity
GO:0034594	0.57	phosphatidylinositol trisphosphate phosphatase activity
GO:0004721	0.56	phosphoprotein phosphatase activity
GO:0016314	0.55	phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase 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 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	1.00	regulation of cellular process
GO:0048519	1.00	negative regulation of biological process
GO:0046856	1.00	phosphatidylinositol dephosphorylation
GO:0023051	0.99	regulation of signaling
GO:0010646	0.99	regulation of cell communication
GO:0044767	0.94	single-organism developmental process
GO:0050793	0.89	regulation of developmental process
GO:2000026	0.88	regulation of multicellular organismal development
GO:0009966	0.88	regulation of signal transduction
GO:0048856	0.83	anatomical structure development
GO:1902531	0.80	regulation of intracellular signal transduction
GO:0051896	0.79	regulation of protein kinase B signaling
GO:0048869	0.75	cellular developmental process
GO:0022603	0.75	regulation of anatomical structure morphogenesis
GO:0016043	0.75	cellular component organization
GO:0051241	0.74	negative regulation of multicellular organismal process
GO:0051093	0.74	negative regulation of developmental process
GO:0050896	0.74	response to stimulus
GO:0030030	0.73	cell projection organization
GO:0009888	0.67	tissue development
GO:0006950	0.62	response to stress
GO:0007165	0.61	signal transduction
GO:0002376	0.61	immune system process
GO:0048523	0.60	negative regulation of cellular process
GO:0051128	0.58	regulation of cellular component organization
GO:0065008	0.57	regulation of biological quality
GO:0051129	0.56	negative regulation of cellular component organization
GO:0042127	0.56	regulation of cell proliferation
GO:0023057	0.56	negative regulation of signaling
GO:0010648	0.56	negative regulation of cell communication
GO:0051716	0.55	cellular response to stimulus
GO:0033554	0.54	cellular response to stress
GO:0048468	0.53	cell development
GO:0002252	0.53	immune effector process
GO:0043170	0.52	macromolecule metabolic process
GO:0044260	0.51	cellular macromolecule metabolic process
GO:0031175	0.51	neuron projection development
GO:0032879	0.50	regulation of localization

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:0005737	1.00	cytoplasm
GO:0043226	0.69	organelle
GO:0043229	0.68	intracellular organelle
GO:0043227	0.68	membrane-bounded organelle
GO:0043231	0.67	intracellular membrane-bounded organelle
GO:0005634	0.64	nucleus
GO:0044446	0.59	intracellular organelle part
GO:0016020	0.57	membrane
GO:0044428	0.54	nuclear part
GO:0044425	0.52	membrane part
GO:0005654	0.51	nucleoplasm

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	2zkmX	0.406	3.35	0.073	0.519	3.1.4.11	NA
2	0.060	2enqA	0.420	3.69	0.065	0.547	2.7.1.153	NA
3	0.060	1qwlA	0.421	4.71	0.021	0.641	1.11.1.6	NA
4	0.060	1gttD	0.391	5.46	0.075	0.646	4.1.1.68 5.3.3.10	NA
5	0.060	3hhsB	0.401	6.14	0.059	0.741	1.14.18.1	186

	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:

No Binding sites was predicted

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.