D-I-TASSER P0DPI3-D1

D-I-TASSER results for P0DPI3-D1

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

Input Sequence in FASTA format

>P0DPI3 (272 residues)
MGRVRNRATAQRRRRKRPGDPPAACAAIAVTGASRAQCPRVQVGVGSHAAAKRWLGRWRR
KRRWRRVRKAGPRDLLPSAPTPDPPGPAPSPKDLDLGAQRERWETFRKLRGLSCEGAAKV
LLDTFEYPGLVHHTGGCHCGAVRFAVWAPADLRVVDCSCRLCRKKQHRHFLVPASRFTLL
QGAESIVTYRSNTHPALHSFCSRCGVQSFHAAVSDPRVYGVAPHCLDEGTVRSVVIEEVG
GGDPGEEAAEEHKAIHKTSSQSAPACPREQEQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MGRVRNRATAQRRRRKRPGDPPAACAAIAVTGASRAQCPRVQVGVGSHAAAKRWLGRWRRKRRWRRVRKAGPRDLLPSAPTPDPPGPAPSPKDLDLGAQRERWETFRKLRGLSCEGAAKVLLDTFEYPGLVHHTGGCHCGAVRFAVWAPADLRVVDCSCRLCRKKQHRHFLVPASRFTLLQGAESIVTYRSNTHPALHSFCSRCGVQSFHAAVSDPRVYGVAPHCLDEGTVRSVVIEEVGGGDPGEEAAEEHKAIHKTSSQSAPACPREQEQ
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCHHHCCCCCCCCCCSSSSSSSSCCCSSSSSSSCCCCCSCCCCCCCCCCCCCCSSSSSCCCCSSSCCCCCCSSSSCCCCCSSSCCCCCCCCCCCCSCCCCCCSSSSSSSSCCCCCHHHCSSSSCCCCCCHHHCHCCCCCCCCCCCCCCCCCCCCCCC
Confidence	96323565445334579989832244333344211117624641455566553120146776411011246777777899999987557632244453135555321245556455122124667888741796587357389999806986223664641103324069986122189638887247854999579803799885332122689975998621338998101437972899834551101542111356788988532359
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MGRVRNRATAQRRRRKRPGDPPAACAAIAVTGASRAQCPRVQVGVGSHAAAKRWLGRWRRKRRWRRVRKAGPRDLLPSAPTPDPPGPAPSPKDLDLGAQRERWETFRKLRGLSCEGAAKVLLDTFEYPGLVHHTGGCHCGAVRFAVWAPADLRVVDCSCRLCRKKQHRHFLVPASRFTLLQGAESIVTYRSNTHPALHSFCSRCGVQSFHAAVSDPRVYGVAPHCLDEGTVRSVVIEEVGGGDPGEEAAEEHKAIHKTSSQSAPACPREQEQ
Prediction	75435754444554574446364314314344364443230411223413443222423552314424644446424752435444544445425364546414524634524474224222622637414414024134202020405462511201032022200000002344030222464323142445404121234002302132443231011100004614166042330234423451165253145367563444566588
	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                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCHHHCCCCCCCCCCSSSSSSSSCCCSSSSSSSCCCCCSCCCCCCCCCCCCCCSSSSSCCCCSSSCCCCCCSSSSCCCCCSSSCCCCCCCCCCCCSCCCCCCSSSSSSSSCCCCCHHHCSSSSCCCCCCHHHCHCCCCCCCCCCCCCCCCCCCCCCC
MGRVRNRATAQRRRRKRPGDPPAACAAIAVTGASRAQCPRVQVGVGSHAAAKRWLGRWRRKRRWRRVRKAGPRDLLPSAPTPDPPGPAPSPKDLDLGAQRERWETFRKLRGLSCEGAAKVLLDTFEYPGLVHHTGGCHCGAVRFAVWAPADLRVVDCSCRLCRKKQHRHFLVPASRFTLLQGAESIVTYRSNTHPALHSFCSRCGVQSFHAAVSDPRVYGVAPHCLDEGTVRSVVIEEVGGGDPGEEAAEEHKAIHKTSSQSAPACPREQEQ

1x6mA

0.17

0.10

3.39

1.18

CEthreader

--------------------------------------------------------------------------------------------------------GHMVDTSGVKIHPAVDNGIKPAQPGFAGGTLHCKCSPVRVAVRAQT-AHNHVCGCTKCWKIFSQVAVVGRDALEVLEGAEKLEIVNAEAPI-QRHRCRDCGVHMYGRIENFYGLDFVHTELSDEDGWSAPEFAAFVSSIIESGVDPSRMEAIRARLRELGLEPYDALS

3facA

0.30

0.12

3.57

1.26

SPARKS-K

------------------------------------------------------------------------------------------------------------------------------------MKGTCHCGAVEIEVELLGFADARRCDCSFCRRRGAIAATARLSDLRVVRGAENLTLYQFGTRTAKHWFCRTCGIYTHHQRRSNPEEYGVNVAILEGVNPRDLGEVPWT--------------------------------

3facA

0.33

0.11

3.43

2.15

CNFpred

------------------------------------------------------------------------------------------------------------------------------------MKGTCHCGAVEIEVELLNFADARRCDCSFCRRRGAIAATARLSDLRVVRGAENLTLYQFGTRTAKHWFCRTCGIYTHHQRRSNPEEYGVNVAILE---------------------------------------------

1x6mA

0.18

0.11

3.47

1.18

MapAlign

----------------------------------------------------------------------------------------------------------MVDTSGVKIHPAVDNGIKPAQPGFAGGTLHCKCNPVRVAVRA-QTAHNHVCGCTKCWAIFSQVAVVGRDALEVLEGAEKLEIVNAEA-PIQRHRCRDCGVHMYGRIENFYGLDFVHTELSD--EDGWSAPEFAAFVSSEPYDALSPPLMDAIATHIAKRSGALAA-

3facA

0.30

0.12

3.57

4.05

HHsearch

------------------------------------------------------------------------------------------------------------------------------------MKGTCHCGAVEIEVELLNFADARRCDCSFCRRRGAIAATARLSDLRVVRGAENLTLYQFGTRTAKHWFCRTCGIYTHHQRRSNPEEYGVNVAILEGVNPRDLGEVPWT--------------------------------

3facA

0.30

0.12

3.57

1.05

CEthreader

------------------------------------------------------------------------------------------------------------------------------------MKGTCHCGAVEIEVELLNGFDARRCDCSFCRRRGAIAATARLSDLRVVRGAENLTLYQFGTRTAKHWFCRTCGIYTHHQRRSNPEEYGVNVAILEGVNPRDLGEVPWT--------------------------------

1x6mA

0.16

0.10

3.28

1.19

SPARKS-K

----------------------------------------------------------------------------------------------------------GHMVDTSGVKIHPAVDNGIKPAQFAGGTLHCKCSPVRVAVRAQTA-HNHVCGCTKCWKPFSQVAVVGRDALEVLEGAEKLEIVN-AEAPIQRHRCRDCGVHMYGRIHPFYGLDFVHTELSDEDGWSAPEFAAFVSSIIESRMEAIRARLRELGLEPYDALSPPLMD

1x6mA

0.24

0.09

2.86

2.06

CNFpred

-------------------------------------------------------------------------------------------------------------------------------------TLHCKCSPVRVAVRAQ-TAHNHVCGCTKCWKP-SQVAVVGRDALEVLEGAEKLEIVNAE-APIQRHRCRDCGVHMYGRIE-FYGLDFVHTELSDEDGWSAPEFAAFV--------------------------------

1x6mA

0.20

0.12

3.87

3.54

HHsearch

----------------------------------------------------------------------------------------------------------GHMVDTSGVKIHP-AVDNGIKPAQPGFAGGCKCSTVRVAVRAQ-TAHNHVCGCTKCWKPGAQVAVVGRDALEVLEGAEKLEIVNAE-APIQRHRCRDCGVHMYGRIENFYGLDFVHTELSDEDGWSAPEFAAFVSSISGV-DPSRMEAIRELGLEPYDALSPPLMD

5j6pB

0.09

0.03

1.24

0.51

CEthreader

------------------------------------------------------------------------------------------------------------------------------ESQPSVFQ----CKKCFQIVGDSNAWVISH--------REYLSFTLSDAVENSVRVEDTFKRSDDGLCVYSELSCTRCNEVIGKVYNSTRDMYTFSMDKLQAYQLGN---------------------------------------

(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	0.6133

(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	6eoqA	0.42	5.66	0.045	0.658	model1_6eoqA.pdb.gz
2	6trwA	0.41	5.79	0.026	0.669	model1_6trwA.pdb.gz
3	5oljA	0.41	5.73	0.063	0.673	model1_5oljA.pdb.gz
4	2ecfA	0.41	6.15	0.055	0.699	model1_2ecfA.pdb.gz
5	3g0bB	0.41	5.88	0.051	0.669	model1_3g0bB.pdb.gz
6	4ztxA	0.41	6.31	0.069	0.695	model1_4ztxA.pdb.gz
7	4hvtA	0.40	5.59	0.048	0.643	model1_4hvtA.pdb.gz
8	4ffvA	0.40	5.92	0.048	0.662	model1_4ffvA.pdb.gz
9	1z68A	0.40	5.77	0.030	0.654	model1_1z68A.pdb.gz
10	4f9iA	0.40	6.03	0.034	0.665	model1_4f9iA.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:0003824	0.84	catalytic activity
GO:0017171	0.54	serine hydrolase 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:0009987	0.93	cellular process
GO:0016043	0.90	cellular component organization
GO:0050794	0.87	regulation of cellular process
GO:0034622	0.86	cellular macromolecular complex assembly
GO:0006996	0.86	organelle organization
GO:0034508	0.82	centromere complex assembly
GO:0033044	0.82	regulation of chromosome organization
GO:0032467	0.82	positive regulation of cytokinesis
GO:0031508	0.82	pericentric heterochromatin assembly
GO:0001667	0.82	ameboidal-type cell migration

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:0032991	0.99	macromolecular complex
GO:0044446	0.97	intracellular organelle part
GO:0044444	0.96	cytoplasmic part
GO:0043234	0.96	protein complex
GO:0043226	0.93	organelle
GO:0043229	0.92	intracellular organelle
GO:0043232	0.90	intracellular non-membrane-bounded organelle
GO:0005737	0.90	cytoplasm
GO:0043227	0.89	membrane-bounded organelle
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0005856	0.87	cytoskeleton
GO:0044428	0.86	nuclear part
GO:0005634	0.86	nucleus
GO:0051233	0.84	spindle midzone
GO:0015630	0.84	microtubule cytoskeleton
GO:0005654	0.84	nucleoplasm
GO:0000776	0.84	kinetochore
GO:0044425	0.82	membrane part
GO:0098796	0.74	membrane protein complex
GO:0005747	0.73	mitochondrial respiratory chain complex I

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	2ajtA	0.366	6.57	0.029	0.662	5.3.1.4	NA
2	0.060	2gv9B	0.353	5.48	0.034	0.551	2.7.7.7	181,221
3	0.060	2fhcA	0.375	6.13	0.050	0.636	3.2.1.41	145
4	0.060	1fuiA	0.360	6.11	0.047	0.607	5.3.1.25	NA
5	0.060	1u22A	0.399	6.12	0.041	0.680	2.1.1.14	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	0.01	1x70A	0.407	6.05	0.057	0.680	1.06	UUU	complex1.pdb.gz	135,142,180,181,182
2	0.01	2bgnB	0.329	6.53	0.036	0.596	0.83	UUU	complex2.pdb.gz	199,201,204,206,208
3	0.01	2qoeA	0.406	6.02	0.061	0.676	0.45	UUU	complex3.pdb.gz	142,183,184
4	0.01	1tk3B	0.406	5.81	0.057	0.658	0.73	NDG	complex4.pdb.gz	143,179,180

	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.