D-I-TASSER O00408-D1

D-I-TASSER results for O00408-D1

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

Input Sequence in FASTA format

>O00408 (201 residues)
MGQACGHSILCRSQQYPAARPAEPRGQQVFLKPDEPPPPPQPCADSLQDALLSLGSVIDI
SGLQRAVKEALSAVLPRVETVYTYLLDGESQLVCEDPPHELPQEGKVREAIISQKRLGCN
GLGFSDLPGKPLARLVAPLAPDTQVLVMPLADKEAGAVAAVILVHCGQLSDNEEWSLQAV
EKHTLVALRRVQVLQQRGPRE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MGQACGHSILCRSQQYPAARPAEPRGQQVFLKPDEPPPPPQPCADSLQDALLSLGSVIDISGLQRAVKEALSAVLPRVETVYTYLLDGESQLVCEDPPHELPQEGKVREAIISQKRLGCNGLGFSDLPGKPLARLVAPLAPDTQVLVMPLADKEAGAVAAVILVHCGQLSDNEEWSLQAVEKHTLVALRRVQVLQQRGPRE
Prediction	CCCCCCCSSSSCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCCCCCSSSSSSSCCCCCSSCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCHHHCCCCHHHHHCCCCCCCCSSSSSSSSCCCCCCSSSSSSSSCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence	986555302322566887889887654011268989999971556789999987535248999999999999974554338999976987433269964466335478998753544248999555556324443146889966999984513568178999985035674147788898889999999999999751489
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MGQACGHSILCRSQQYPAARPAEPRGQQVFLKPDEPPPPPQPCADSLQDALLSLGSVIDISGLQRAVKEALSAVLPRVETVYTYLLDGESQLVCEDPPHELPQEGKVREAIISQKRLGCNGLGFSDLPGKPLARLVAPLAPDTQVLVMPLADKEAGAVAAVILVHCGQLSDNEEWSLQAVEKHTLVALRRVQVLQQRGPRE
Prediction	745312330103265264555444424522143766453454145314400230011021530351035004400340420010003562312063345612753403501453440506714476236431340133135433000000024524300000001014134555330420342021003203313564588
	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

CCCCCCCSSSSCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCCCCCSSSSSSSCCCCCSSCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCHHHCCCCHHHHHCCCCCCCCSSSSSSSSCCCCCCSSSSSSSSCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
MGQACGHSILCRSQQYPAARPAEPRGQQVFLKPDEPPPPPQPCADSLQDALLSLGSVIDISGLQRAVKEALSAVLPRVETVYTYLLDGESQLVCEDPPHELPQEGKVREAIISQKRLGCNGLGFSDLPGKPLARLVAPLAPDTQVLVMPLADKEAGAVAAVILVHCGQLSDNEEWSLQAVEKHTLVALRRVQVLQQRGPRE

3ibjA

0.18

0.14

4.54

1.29

HHsearch

---------------------------------------YTDRDRKILQLCGELY-DLDASSLQLKVLQYLQQETR-ASRCCLLLVSEDNQLSCGDEEVSFPLTGCLGQVVEDKKSIQLKDLTSEDVQ--QLQSML--GCELQAMLCVPVISRATDQVVALACAFNDLFTDEDEHVIQHCFHYTSTVLTSTLAFQKEQKLK

4mcwA

0.11

0.08

2.91

1.19

CNFpred

-------------------------------------------LKILLDYSSKIANEKDLRNVLLFLTDLAKEIM-EADRASIFLYDDKKTLWTIVDRIEIDAKGIAGYVFRTGEILNIPDAYKDPRFDRDIDKR----YRTRTILAVPLFDR-KQNIIGVFQVINKVFTEEDIELLRHISLYASSTIENAILYEKLKKAH

4ourA

0.10

0.08

3.09

1.00

DEthreader

-------------------QPFGMLEPARTE----DPAIAAVQQKLAVRAISQLQALGDIKLLCDTVVESVRDLT-GYDRVMVYKFHE-DEHGEVYLHYPATD-IPQ-----------SRFLFNLVTLRAPHGCHSYMAG-IASLAMAVIINGS-MRLWGLVVCHHRCIPFPLRYACEFLMQAFGLQLNMELQLALQMSRV

5hl6A

0.13

0.09

3.28

0.94

SPARKS-K

----------------------------------------ASKAELYATLAEQARSLVDLIANAANFSALVYHSLDRLNWAGFYFFDGTEVVGPFQACVRIAGKGVCGTAAQTRQTQVVRDVHAFPGHIACDAAS-------ESEIVVPLVAAD-GTLIGVWDVDSPVFDDEDRSGMEALCRVFVEHAWQKARD-------

4mcwA

0.11

0.08

3.05

0.71

MapAlign

-----------------------------------------RKLKILLDYSSKIANEKDLRNVLLFLTDLAKEIM-EADRASIFLYDQKKTLWTGVDRIEIDAKGIAGYVFRTGEILNIPDA--YKDPRFDRDIDKRTGYRTRTILAVPLFD-RKQNIIGVFQVINKLFTEEDIELLRHISLYASSTIENAILYEKLKKA-

3ibjA1

0.15

0.12

4.00

0.49

CEthreader

----------------------------------------YTDRDRKILQLCGELYDLDASSLQLKVLQYLQQETR-ASRCCLLLVSEDNLQLSCKVEVSFPLTGCLGQVVEDKKSIQLKDLTSEDVQQLQ----SMLGCELQAMLCVPVISRATDQVVALACAFNKLFTDEDEHVIQHCFHYTSTVLTSTLAFQKEQKLK

3lfvA

0.15

0.13

4.55

0.59

MUSTER

MERKISASEF--DRPLRPIVVKDSEGTVSFLS-DQ--------SSRLLELVKDISSHLDVTALCHKIFLHIHGLIS-ADRYSLFLVCEDSSLISRSTLEEVWNKGIVGHVAALGEPLNIKDAYEDPRFNAEVDQITGY--KTQSILCMPIKNHR-EEVVGVAQAI-GTFTEKDEKDFAAYLAFCGIVLHNAQLYETSLLEN

4dmzA1

0.17

0.10

3.44

1.00

HHsearch

------------------------------------------NDQSLRSSLLGLRQLLRELPLDALAETVLALLAGSLRIAGLYRVRHDRQPLAGEMPVLDADDLLVRTCLERGELVSVRA----------------------LQVCVPLVDT-DGRILALLAVEQMVFNERTFSLLAILAGHIADLLQ------------

4qprA

0.15

0.09

3.18

0.90

FFAS-3D

----------------------------------------------------ALAVGRSPQDIAATSEQFIASTFH--ARSQVLLPDDNGKLQPLTHPQGTPWDDAIAQWSFDKGL---------------PAGAGTDTLPGVPYQILPLKSGEK--TYGLVVVEPGNLIPEQQRLLETFTLLVANALERLTKLAAA----

6fhtA1

0.09

3.40

0.93

EigenThreader

HSGEQEPTVLRGQTLAALLPEQWPALQAALPPGCPDEAWDSTGPHALRNAMFALESAPNLRALAEVATQTVRELTGFDR-VMLYKFAPDATGEVIFLGHASDIPAQARALYTRHLLRLTRAAAVPLDPVPLGGAVLRATSGVGSSLSVSVVVG--GQLWGLIACHHQTPYVLLRTTLEYLGRLLSLQVQVKEAADVAAEVA

(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	0.6063

(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	4ourA	0.72	3.07	0.084	0.876	model1_4ourA.pdb.gz
2	6fhtA	0.71	3.48	0.099	0.886	model1_6fhtA.pdb.gz
3	3ibjA	0.70	2.54	0.116	0.796	model1_3ibjA.pdb.gz
4	4o01A	0.70	3.52	0.106	0.871	model1_4o01A.pdb.gz
5	5oy5A	0.70	3.28	0.103	0.851	model1_5oy5A.pdb.gz
6	4r70A	0.69	3.45	0.053	0.856	model1_4r70A.pdb.gz
7	3c2wC	0.69	3.72	0.089	0.886	model1_3c2wC.pdb.gz
8	6baoA	0.69	3.49	0.131	0.881	model1_6baoA.pdb.gz
9	6g1yA	0.69	3.37	0.074	0.871	model1_6g1yA.pdb.gz
10	6ptqA	0.69	3.30	0.111	0.866	model1_6ptqA.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:0030553	1.00	cGMP binding
GO:0008144	1.00	drug binding
GO:0004118	1.00	cGMP-stimulated cyclic-nucleotide phosphodiesterase 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:0097011	1.00	cellular response to granulocyte macrophage colony-stimulating factor stimulus
GO:0071321	1.00	cellular response to cGMP
GO:0046069	1.00	cGMP catabolic process
GO:0043117	1.00	positive regulation of vascular permeability
GO:0043116	1.00	negative regulation of vascular permeability
GO:0036006	1.00	cellular response to macrophage colony-stimulating factor stimulus
GO:0035690	1.00	cellular response to drug
GO:0033159	1.00	negative regulation of protein import into nucleus, translocation
GO:0019934	1.00	cGMP-mediated signaling
GO:0019933	1.00	cAMP-mediated signaling
GO:0006198	1.00	cAMP catabolic process
GO:0000122	1.00	negative regulation of transcription from RNA polymerase II promoter
GO:0048518	0.61	positive regulation of biological process
GO:0032502	0.61	developmental process
GO:0048856	0.60	anatomical structure development
GO:0048583	0.60	regulation of response to stimulus
GO:0044767	0.60	single-organism developmental process
GO:0006810	0.60	transport
GO:0080134	0.59	regulation of response to stress
GO:0048584	0.59	positive regulation of response to stimulus
GO:0048468	0.59	cell development
GO:0019220	0.59	regulation of phosphate metabolic process
GO:0015031	0.59	protein transport
GO:0009628	0.59	response to abiotic stimulus
GO:0071260	0.58	cellular response to mechanical stimulus
GO:0061028	0.58	establishment of endothelial barrier
GO:0050729	0.58	positive regulation of inflammatory response
GO:0030818	0.58	negative regulation of cAMP biosynthetic process
GO:0006626	0.58	protein targeting to mitochondrion

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:0048471	1.00	perinuclear region of cytoplasm
GO:0005886	1.00	plasma membrane
GO:0005634	1.00	nucleus
GO:0044446	0.63	intracellular organelle part
GO:0005829	0.63	cytosol
GO:0044425	0.61	membrane part
GO:0097458	0.59	neuron part
GO:0044459	0.59	plasma membrane part
GO:0005794	0.59	Golgi apparatus
GO:0005759	0.59	mitochondrial matrix
GO:0005737	0.59	cytoplasm
GO:0042734	0.58	presynaptic membrane
GO:0005783	0.58	endoplasmic reticulum

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	0.068	1f5mB	0.634	2.20	0.093	0.721	1.8.4.14	NA
2	0.060	2k2nA	0.521	2.89	0.159	0.627	2.7.13.3	NA
3	0.060	3ifsE	0.447	5.21	0.030	0.726	5.3.1.9	NA
4	0.060	1b8aB	0.432	4.91	0.054	0.662	6.1.1.12	NA
5	0.060	1fo4A	0.423	5.05	0.041	0.672	1.17.1.4	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	0.08	2vzwB	0.550	2.53	0.137	0.632	0.69	UUU	complex1.pdb.gz	80,81,105,106,107,126,127,129,130,131,142,145,163,165
2	0.02	3ko6A	0.634	2.19	0.093	0.721	0.75	SME	complex2.pdb.gz	84,101,105,106,107,133,145,163,165
3	0.01	3sztB	0.536	3.36	0.079	0.682	0.65	OHN	complex3.pdb.gz	83,85,86,97,106,107,110,119,158,159,160,162

	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.