D-I-TASSER O00408-D2

D-I-TASSER results for O00408-D2

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

Input Sequence in FASTA format

>O00408 (186 residues)
APRAVQNPPEGTAEDQKGGAAYTDRDRKILQLCGELYDLDASSLQLKVLQYLQQETRASR
CCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTGCLGQVVEDKKSIQLKDLTSEDVQQLQS
MLGCELQAMLCVPVISRATDQVVALACAFNKLEGDLFTDEDEHVIQHCFHYTSTVLTSTL
AFQKEQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| APRAVQNPPEGTAEDQKGGAAYTDRDRKILQLCGELYDLDASSLQLKVLQYLQQETRASRCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTGCLGQVVEDKKSIQLKDLTSEDVQQLQSMLGCELQAMLCVPVISRATDQVVALACAFNKLEGDLFTDEDEHVIQHCFHYTSTVLTSTLAFQKEQ
Prediction	CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCSSSSSSSSCCCCSSSSSSSCCCCCCCCCCCCCHHHHHHHHHHCCSSSSCCCCCCCCHHHCCCCCCCCCSSSSSSSSSCCCCSSSSSSSSSSCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence	996546898521455788999999999999999999970199999999999999979984999999799998999996786544310146420899999719819964633296212023359865559998425078995999999995599999999999999999999999999999999739
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| APRAVQNPPEGTAEDQKGGAAYTDRDRKILQLCGELYDLDASSLQLKVLQYLQQETRASRCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTGCLGQVVEDKKSIQLKDLTSEDVQQLQSMLGCELQAMLCVPVISRATDQVVALACAFNKLEGDLFTDEDEHVIQHCFHYTSTVLTSTLAFQKEQ
Prediction	855437434454355464345335224401500440363404400430052026104053001000267442000101445426542402141001201535310304203614255246446241200000002344753000000000246574036402400420042001003104215658
	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                 140                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCSSSSSSSSCCCCSSSSSSSCCCCCCCCCCCCCHHHHHHHHHHCCSSSSCCCCCCCCHHHCCCCCCCCCSSSSSSSSSCCCCSSSSSSSSSSCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
APRAVQNPPEGTAEDQKGGAAYTDRDRKILQLCGELYDLDASSLQLKVLQYLQQETRASRCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTGCLGQVVEDKKSIQLKDLTSEDVQQLQSMLGCELQAMLCVPVISRATDQVVALACAFNKLEGDLFTDEDEHVIQHCFHYTSTVLTSTLAFQKEQ

3ibjA

0.20

0.19

6.01

1.33

DEthreader

---RADHFHSTLTSLFQKEQKLKCECQALLQVAKNLFTLDVSVLLQEIITEARNLSNAEICSVFLLDQ--NELVAKVFD----SYEIRIPDQGIAGHVATTGQILNIPDAYAHPLF---S-TGFRTRNILCFPIKNEN-QEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVN

3ibjA1

1.00

0.89

24.84

1.81

SPARKS-K

---------------------YTDRDRKILQLCGELYDLDASSLQLKVLQYLQQETRASRCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTGCLGQVVEDKKSIQLKDLTSEDVQQLQSMLGCELQAMLCVPVISRATDQVVALACAFNKLEGDLFTDEDEHVIQHCFHYTSTVLTSTLAFQKEQ

3trcA

0.16

0.13

4.49

0.71

MapAlign

---------------------SNANLKILRQITQEVNAANLEQALKLVVVRLCEALPADACSLFICDDVHGEYVLATQGLNSQVGKLRLKFGGLIGLVGEREEPINLADAPLHPAYKHRPELGEEYHGFLGIPIIE--QGELLGILVIQQLE-SHHFAEEEEAFCVTLAIHLAAEIAHARAGAL--

3trcA

0.14

0.12

4.20

0.52

CEthreader

---------------------SNANLKILRQITQEVNAANLEQALKLVVVRLCEALPADACSLFICDDVHGEYVLATQGLNSQVGKLRLKFGGLIGLVGEREEPINLADAPLHPAYKHPELGEEDYHGFLGIPIIE--QGELLGILVIQQL-ESHHFAEEEEAFCVTLAIHLAAEIAHARAKGAL-

3ibjA1

1.00

0.89

24.84

1.64

MUSTER

---------------------YTDRDRKILQLCGELYDLDASSLQLKVLQYLQQETRASRCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTGCLGQVVEDKKSIQLKDLTSEDVQQLQSMLGCELQAMLCVPVISRATDQVVALACAFNKLEGDLFTDEDEHVIQHCFHYTSTVLTSTLAFQKEQ

3ibjA

0.21

0.20

6.33

1.90

HHsearch

VPVIEGDLFTDEDLAFQKEQKLKCECQALLQVAKNLFHLDVSVLLQEIITEARNLSNAEICSVFLLDQ--NELVAKVFGGVVESYEIRIPADGIAGHVATTGQILNIPDAYAHPLF----STGFRTRNILCFPIKNE-NQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVN

3ibjA1

1.00

0.89

24.84

2.26

FFAS-3D

---------------------YTDRDRKILQLCGELYDLDASSLQLKVLQYLQQETRASRCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTGCLGQVVEDKKSIQLKDLTSEDVQQLQSMLGCELQAMLCVPVISRATDQVVALACAFNKLEGDLFTDEDEHVIQHCFHYTSTVLTSTLAFQKEQ

3lfvA1

0.20

0.19

6.20

0.95

EigenThreader

ASEFDRPLRPIVVKDSEGTVSFLSSSRLLELVKDISSHLDVTALCHKIFLHIHG---LISYSLFLVCESSNDLISRLFDVVSNNCIRLEWNKGIVGHVAALGEPLNIKDAYEDPRFNVDQITGYKTQSILCMPIKN-HREEVVGVAQAINKGNGGTFTEKDEKDFAAYLAFCGIVLHNAQLYETSL

1mc0A

0.92

0.81

22.81

1.65

CNFpred

---------------------YTDHDRKILQLCGELFDLDATSLQLKVLQYLQQETQATHCCLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTGRLGQVVEDKQCIQLKDLTSDDVQQLQNMLGCELQAMLCVPVISRATDQVVALACAFNKLGGDFFTDEDEHVIQHCFHYTGTVLTSTLAFQKEQ

3lfvA

0.12

0.11

3.82

1.33

DEthreader

-----HAAFGIHNAQYETSLLENKRNQVLLDLASLIFEQSLEVILKKIAATIISFMQVQKCTIFIVDDCSDSFSVFHMECEELEKSINY---MYAQYVKNTMEPLNIPDVSKDFPW-------QCIRSLLCTPIKNGKKNKVIGVCQLVNKMKVKPFNRNDEQFLEAFVIFCGLGIQNTQMYEAVE

(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	0.8325

(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	3lfvA	0.78	2.68	0.121	0.909	model1_3lfvA.pdb.gz
2	3trcA	0.78	1.96	0.144	0.860	model1_3trcA.pdb.gz
3	3ibjA	0.77	2.36	0.202	0.871	model1_3ibjA.pdb.gz
4	5w10A	0.77	2.29	0.171	0.882	model1_5w10A.pdb.gz
5	6x88A	0.75	2.55	0.219	0.909	model1_6x88A.pdb.gz
6	7jsnA	0.75	2.87	0.179	0.909	model1_7jsnA.pdb.gz
7	4mcwA	0.74	2.43	0.161	0.866	model1_4mcwA.pdb.gz
8	3ci6B	0.74	1.92	0.162	0.823	model1_3ci6B.pdb.gz
9	1vhmB	0.72	2.44	0.135	0.833	model1_1vhmB.pdb.gz
10	3oovA	0.71	2.19	0.119	0.812	model1_3oovA.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:0004114	1.00	3',5'-cyclic-nucleotide phosphodiesterase activity
GO:1901363	0.96	heterocyclic compound binding
GO:0097159	0.96	organic cyclic compound binding
GO:0032555	0.95	purine ribonucleotide binding
GO:0030553	0.94	cGMP binding
GO:0004118	0.94	cGMP-stimulated cyclic-nucleotide phosphodiesterase activity
GO:0008144	0.78	drug 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	0.98	single-organism process
GO:0008152	0.98	metabolic process
GO:0007165	0.98	signal transduction
GO:0044763	0.97	single-organism cellular process
GO:0006139	0.97	nucleobase-containing compound metabolic process
GO:0050896	0.96	response to stimulus
GO:0009150	0.96	purine ribonucleotide metabolic process
GO:0065008	0.93	regulation of biological quality
GO:0051716	0.93	cellular response to stimulus
GO:0046068	0.93	cGMP metabolic process
GO:0046058	0.93	cAMP metabolic process
GO:0003008	0.93	system process
GO:0046069	0.92	cGMP catabolic process
GO:0006198	0.92	cAMP catabolic process
GO:0080090	0.91	regulation of primary metabolic process
GO:0060255	0.91	regulation of macromolecule metabolic process
GO:0035556	0.91	intracellular signal transduction
GO:0031323	0.91	regulation of cellular metabolic process
GO:0097011	0.90	cellular response to granulocyte macrophage colony-stimulating factor stimulus
GO:0071321	0.90	cellular response to cGMP
GO:0043117	0.90	positive regulation of vascular permeability
GO:0043116	0.90	negative regulation of vascular permeability
GO:0036006	0.90	cellular response to macrophage colony-stimulating factor stimulus
GO:0035690	0.90	cellular response to drug
GO:0033159	0.90	negative regulation of protein import into nucleus, translocation
GO:0019934	0.90	cGMP-mediated signaling
GO:0019933	0.90	cAMP-mediated signaling
GO:0000122	0.90	negative regulation of transcription from RNA polymerase II promoter
GO:0009628	0.60	response to abiotic stimulus
GO:0009605	0.60	response to external stimulus
GO:0032502	0.59	developmental process
GO:0048856	0.58	anatomical structure development
GO:0071214	0.57	cellular response to abiotic stimulus
GO:0048583	0.57	regulation of response to stimulus
GO:0048518	0.57	positive regulation of biological process
GO:0044767	0.57	single-organism developmental process
GO:0048468	0.56	cell development
GO:0032101	0.56	regulation of response to external stimulus
GO:0006810	0.56	transport
GO:0080134	0.55	regulation of response to stress
GO:0071702	0.55	organic substance transport
GO:0048584	0.55	positive regulation of response to stimulus
GO:0019220	0.55	regulation of phosphate metabolic process
GO:0008104	0.55	protein localization
GO:0071260	0.54	cellular response to mechanical stimulus
GO:0061028	0.54	establishment of endothelial barrier
GO:0050729	0.54	positive regulation of inflammatory response
GO:0030818	0.54	negative regulation of cAMP biosynthetic process
GO:0006626	0.54	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:0044464	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0043226	0.94	organelle
GO:0016020	0.94	membrane
GO:0043229	0.93	intracellular organelle
GO:0043227	0.93	membrane-bounded organelle
GO:0044444	0.92	cytoplasmic part
GO:0005886	0.92	plasma membrane
GO:0005634	0.92	nucleus
GO:0048471	0.88	perinuclear region of cytoplasm
GO:0044422	0.61	organelle part
GO:0097458	0.60	neuron part
GO:0005829	0.60	cytosol
GO:0044425	0.59	membrane part
GO:0044446	0.58	intracellular organelle part
GO:0044459	0.57	plasma membrane part
GO:0005737	0.57	cytoplasm
GO:0098590	0.56	plasma membrane region
GO:0042734	0.53	presynaptic membrane
GO:0005794	0.53	Golgi apparatus
GO:0005783	0.53	endoplasmic reticulum
GO:0005759	0.53	mitochondrial matrix

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	0.119	1f5mB	0.725	2.57	0.098	0.844	1.8.4.14	94,122,151
2	0.113	2zmfB	0.678	2.73	0.204	0.801	3.1.4.17	58,61,63,66,97,131,162
3	0.113	3dbaB	0.668	2.54	0.286	0.785	3.1.4.35	102,130
4	0.070	2k2nA	0.613	2.87	0.108	0.747	2.7.13.3	89,130,132,145
5	0.060	1fr1A	0.433	4.15	0.054	0.597	3.5.2.6	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	0.78	1mc0A	0.736	2.66	0.847	0.876	1.05	PCG	complex1.pdb.gz	60,61,62,78,93,94,118,119,124,126,129,147
	2	0.24	2vzwB	0.654	2.40	0.189	0.747	0.87	UUU	complex2.pdb.gz	60,61,76,78,79,81,89,93,94,95,114,115,116,119,120,123,126,129,147,149

	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.