D-I-TASSER P02647-D3

D-I-TASSER results for P02647-D3

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

Input Sequence in FASTA format

>P02647 (114 residues)
ARQKLHELQEKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARL
AEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| ARQKLHELQEKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ
Prediction	CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence	714699999999999999999999889999999887899999999999999999935789999999999999999998999999999889889999999999999999976169
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| ARQKLHELQEKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ
Prediction	856426513740552055127415631551374244235403741463155137414531550264046315513631463155137414521550354035215403742578
	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

                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
ARQKLHELQEKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ

4f61I

0.11

4.08

1.50

DEthreader

AEKREHEREVIQRAIEENNNWIKMAKEKLAQKMESNKENREAHFAAMLERLQEKDKHAEEVRQRAIEENNNWIKMAKEKLAQKMESNKENRKYQEAELLKHLAEKREHEREVIQ

6cfeA

0.23

7.16

1.01

SPARKS-K

SEQVQEELLTKLNKLMQRTMEELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLATHLNKLRQRLLEDADDLQKRLAVY

1av1A

0.44

12.84

2.30

HHsearch

WQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAELRQGLLPVLESFKVSFLSALEEYTKKLNTQ

6cfeA

0.21

6.67

1.30

FFAS-3D

SEQVQEQVETKLNKLMQRTMEELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLATHLNKLRQRLLEDADDLQKRLA--

6z47G

0.08

3.13

1.50

DEthreader

RTLEQQVEEMKTQLEELEDELQAAEDAKLRLEVNMQAMKSQFERDLQARDEQNEEKRRQLLKQLHEHETELEDERKQRALAAAAKKKLEVDVKDLESQVDSVNKAREEAIKQRK

4tqlA

0.11

4.08

0.97

SPARKS-K

ARDRMEKLYKEMVELIQKAIELMRKIFQEVKQEVEKAIEEMKKLYDEAKKKIEQMIQQIKKQKMEELLKRAKEEMKKVKDKMEKLLEKLKQIMQEAKQKMEKLLKQLKEEMKKM

2tmaA1

0.11

4.08

0.42

MapAlign

DKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGM

2tmaA1

0.11

4.08

0.36

CEthreader

LEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAK

2a01A

1.00

28.00

0.91

MUSTER

ARQKLHELQEKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ

1av1A

0.24

7.39

2.15

HHsearch

MSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQEKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEYHAKATEH

(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	0.4721

(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	6cfeA	0.85	1.88	0.212	0.983	model1_6cfeA.pdb.gz
2	2kc3A	0.74	3.02	0.211	0.991	model1_2kc3A.pdb.gz
3	2ficB1	0.73	2.80	0.088	0.991	model1_2ficB1.pdb.gz
4	3sogA	0.73	2.78	0.106	0.991	model1_3sogA.pdb.gz
5	6q0xA2	0.73	2.91	0.062	0.983	model1_6q0xA2.pdb.gz
6	2l7bA	0.72	3.00	0.202	1.000	model1_2l7bA.pdb.gz
7	4avmA2	0.72	2.87	0.071	0.983	model1_4avmA2.pdb.gz
8	1uruA	0.71	2.55	0.087	0.912	model1_1uruA.pdb.gz
9	3s84A	0.62	3.68	0.234	0.974	model1_3s84A.pdb.gz
10	1eemA	0.43	3.94	0.100	0.675	model1_1eemA.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:0060228	0.99	phosphatidylcholine-sterol O-acyltransferase activator activity
GO:0017127	0.99	cholesterol transporter activity
GO:0015485	0.99	cholesterol binding
GO:0031210	0.97	phosphatidylcholine binding
GO:0005102	0.67	receptor binding
GO:0070325	0.63	lipoprotein particle receptor binding
GO:0070653	0.61	high-density lipoprotein particle receptor 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:0009987	0.99	cellular process
GO:0044699	0.97	single-organism process
GO:0008152	0.97	metabolic process
GO:0044763	0.96	single-organism cellular process
GO:0044710	0.96	single-organism metabolic process
GO:0044238	0.96	primary metabolic process
GO:0044237	0.96	cellular metabolic process
GO:0043170	0.96	macromolecule metabolic process
GO:0065007	0.83	biological regulation
GO:0050789	0.82	regulation of biological process
GO:0050794	0.80	regulation of cellular process
GO:0048518	0.78	positive regulation of biological process
GO:0031323	0.77	regulation of cellular metabolic process
GO:0044281	0.76	small molecule metabolic process
GO:0031325	0.76	positive regulation of cellular metabolic process
GO:0050896	0.75	response to stimulus
GO:0009891	0.75	positive regulation of biosynthetic process
GO:1901576	0.74	organic substance biosynthetic process
GO:0080090	0.74	regulation of primary metabolic process
GO:0065009	0.74	regulation of molecular function
GO:0031328	0.74	positive regulation of cellular biosynthetic process
GO:0006810	0.74	transport
GO:1901360	0.73	organic cyclic compound metabolic process
GO:0071702	0.73	organic substance transport
GO:0065008	0.73	regulation of biological quality
GO:0051239	0.73	regulation of multicellular organismal process
GO:0048856	0.73	anatomical structure development
GO:0044767	0.73	single-organism developmental process
GO:0044765	0.73	single-organism transport
GO:0043085	0.73	positive regulation of catalytic activity
GO:0016043	0.73	cellular component organization
GO:0006629	0.73	lipid metabolic process
GO:1901617	0.72	organic hydroxy compound biosynthetic process
GO:1901575	0.72	organic substance catabolic process
GO:1901362	0.72	organic cyclic compound biosynthetic process
GO:0065003	0.72	macromolecular complex assembly
GO:0051345	0.72	positive regulation of hydrolase activity
GO:0051049	0.72	regulation of transport
GO:0046890	0.72	regulation of lipid biosynthetic process
GO:0045834	0.72	positive regulation of lipid metabolic process
GO:0044707	0.72	single-multicellular organism process
GO:0044283	0.72	small molecule biosynthetic process
GO:0044255	0.72	cellular lipid metabolic process
GO:0044248	0.72	cellular catabolic process
GO:0042592	0.72	homeostatic process
GO:0042157	0.72	lipoprotein metabolic process
GO:0033554	0.72	cellular response to stress
GO:0033344	0.72	cholesterol efflux
GO:0008610	0.72	lipid biosynthetic process
GO:0008203	0.72	cholesterol metabolic process
GO:0006807	0.72	nitrogen compound metabolic process
GO:0046889	0.71	positive regulation of lipid biosynthetic process
GO:0043691	0.71	reverse cholesterol transport
GO:0042632	0.71	cholesterol homeostasis
GO:0034380	0.71	high-density lipoprotein particle assembly
GO:0034369	0.71	plasma lipoprotein particle remodeling
GO:0033700	0.71	phospholipid efflux
GO:0032374	0.71	regulation of cholesterol transport
GO:0031102	0.71	neuron projection regeneration
GO:0016042	0.71	lipid catabolic process
GO:0010873	0.71	positive regulation of cholesterol esterification
GO:0006695	0.71	cholesterol biosynthetic process
GO:0070328	0.70	triglyceride homeostasis
GO:0051006	0.70	positive regulation of lipoprotein lipase activity
GO:0046470	0.70	phosphatidylcholine metabolic process
GO:0045723	0.70	positive regulation of fatty acid biosynthetic process
GO:0030300	0.70	regulation of intestinal cholesterol absorption
GO:0019433	0.70	triglyceride catabolic process
GO:0010898	0.70	positive regulation of triglyceride catabolic process
GO:0034372	0.66	very-low-density lipoprotein particle remodeling

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:0044421	0.96	extracellular region part
GO:0032991	0.95	macromolecular complex
GO:0072562	0.94	blood microparticle
GO:0042627	0.94	chylomicron
GO:0034364	0.94	high-density lipoprotein particle
GO:0044464	0.65	cell part
GO:0044424	0.54	intracellular 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	0.314	1wu0A	0.485	2.12	0.014	0.597	3.6.3.14	105
2	0.067	2wieA	0.477	2.75	0.027	0.640	3.6.3.14	NA
3	0.067	1a91A	0.519	2.08	0.054	0.649	3.6.3.14	NA
4	0.060	2pfdB	0.599	3.27	0.091	0.921	2.1.2.5 4.3.1.4	NA
5	0.060	1jswB	0.601	3.52	0.083	0.912	4.3.1.1	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:

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
	1	0.06	2rfqC	0.646	2.95	0.108	0.877	0.63	1PS	complex1.pdb.gz	28,51,53,54
	2	0.02	2g381	0.623	3.33	0.087	0.895	0.43	III	complex2.pdb.gz	51,52,54,55,58,59,61,62,65,66,69,73,77,92,95,103,106,110

	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.