D-I-TASSER P22413-D1

D-I-TASSER results for P22413-D1

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

Input Sequence in FASTA format

>P22413 (96 residues)
MERDGCAGGGSRGGEGGRAPREGPAGNGRDRGRSHAAEAPGDPQAAASLLAPMDVGEEPL
EKAARARTAKDPNTYKVLSLVLSVCVLTTILGCIFG

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MERDGCAGGGSRGGEGGRAPREGPAGNGRDRGRSHAAEAPGDPQAAASLLAPMDVGEEPLEKAARARTAKDPNTYKVLSLVLSVCVLTTILGCIFG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCHCHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence	986677777776665676888788877888888877889998235553147632230255642357878998325779999999999999987419
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MERDGCAGGGSRGGEGGRAPREGPAGNGRDRGRSHAAEAPGDPQAAASLLAPMDVGEEPLEKAARARTAKDPNTYKVLSLVLSVCVLTTILGCIFG
Prediction	865644644454456445356544445355544565454545462344313325235522762575554644421410210113023212332348
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCHCHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
MERDGCAGGGSRGGEGGRAPREGPAGNGRDRGRSHAAEAPGDPQAAASLLAPMDVGEEPLEKAARARTAKDPNTYKVLSLVLSVCVLTTILGCIFG

3jbrA

0.14

4.66

0.46

CEthreader

TVENEKPSPCARTGSGRPCTINGSECRGGWPGPNHGITHFDNFGFSMLTVYQCITMEGWTDVLYWVNDAIGNEWPWIYFVTLILLGSFFILNLVLG

5azbA

0.06

2.69

0.47

EigenThreader

GVFLGGRIGYVLFYNGMSFHGGLIGVIVVMIIFARRTKRSFFQVSDFIAPLIPFGLGAGRLGNFINGELWGRPSQLYELLLEGVVLFIILNLYIRK

6ftg3

0.15

0.14

4.56

0.49

FFAS-3D

--------GGIIYDVIVEPPSVGSMTDEHGHQRPVAFLAYREGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLLLFIGFVCVLLSFFMARVFM-

3boiA

0.10

0.08

3.05

1.13

SPARKS-K

GADGAHGVNGCPGTAGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGG-TGVGGRGGKSGTPKGADGAPGAP------------------

3mk4A

0.23

0.05

1.64

0.46

CNFpred

--------------------------------------------------------------------------TRSTVAVYSTCMLVVLLRVQLN

4uxvA

0.08

0.07

2.83

1.00

DEthreader

KSE-DREQSYDDPKLLDCK-----------DGYG-EMKEKGEVAGQSVSKVSIEKQEVKKEHAEYRENLQALRKEELQARETLSNLKKTISETARL

4hn9A

0.07

2.97

0.74

MapAlign

IEAKANTRNIYKLAAPAIVSLPNGTAKEFNTEACVAATPDVVFLPKAVVVNPEDQSLLEECITLVGKITNNAGRAEALNNSIKTFLADNKTNAGGK

3boiA

0.25

0.19

5.80

0.74

MUSTER

HGVNGCPGTGAAGSVGGPGCDGGHGGNGGNGNPGCAGGVGGAGGASGGTGVGGRGGKSGTPKGADGAPGA-P------------------------

1ocoG

0.17

0.06

2.06

0.50

HHsearch

-----------------------------------------------------------ASAAKGDHGGTGARTWRFLTFGLASVALCTL-NSWLH

1xmeA1

0.05

2.41

0.41

CEthreader

LNYGNVDAYPLLKRLLPFVQSYYQGLTLHVYLPARELNMRPNMGLMWLSWWMAFIGLVVAALPLLANEATVGHWAFYLGASVFVLSTWVSIYIVLD

(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	0.5259

(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	6lrdA	0.56	3.84	0.042	0.958	model1_6lrdA.pdb.gz
2	2zxoA	0.56	4.14	0.073	1.000	model1_2zxoA.pdb.gz
3	6c6nA	0.54	4.07	0.022	0.927	model1_6c6nA.pdb.gz
4	2ebaA	0.54	3.58	0.091	0.885	model1_2ebaA.pdb.gz
5	4mndA2	0.54	4.09	0.063	0.906	model1_4mndA2.pdb.gz
6	1sirA	0.52	3.83	0.035	0.865	model1_1sirA.pdb.gz
7	2ix5A	0.51	4.21	0.079	0.896	model1_2ix5A.pdb.gz
8	1ivhA1	0.40	4.57	0.053	0.760	model1_1ivhA1.pdb.gz
9	1w07B	0.39	4.18	0.011	0.688	model1_1w07B.pdb.gz
10	3bjxA	0.38	4.65	0.071	0.750	model1_3bjxA.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:0008270	1.00	zinc ion binding
GO:0005509	1.00	calcium ion binding
GO:0004551	1.00	nucleotide diphosphatase activity
GO:0004528	1.00	phosphodiesterase I activity
GO:1901363	0.76	heterocyclic compound binding
GO:0097159	0.76	organic cyclic compound binding
GO:0097367	0.75	carbohydrate derivative binding
GO:0000166	0.75	nucleotide binding
GO:0005524	0.74	ATP binding
GO:0042802	0.72	identical protein binding
GO:0005102	0.72	receptor binding
GO:0047429	0.71	nucleoside-triphosphate diphosphatase activity
GO:0042803	0.71	protein homodimerization activity
GO:0005158	0.71	insulin 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:0050427	1.00	3'-phosphoadenosine 5'-phosphosulfate metabolic process
GO:0046627	1.00	negative regulation of insulin receptor signaling pathway
GO:0046325	1.00	negative regulation of glucose import
GO:0045719	1.00	negative regulation of glycogen biosynthetic process
GO:0045599	1.00	negative regulation of fat cell differentiation
GO:0032869	1.00	cellular response to insulin stimulus
GO:0031953	1.00	negative regulation of protein autophosphorylation
GO:0030730	1.00	sequestering of triglyceride
GO:0030643	1.00	cellular phosphate ion homeostasis
GO:0030505	1.00	inorganic diphosphate transport
GO:0030308	1.00	negative regulation of cell growth
GO:0030278	1.00	regulation of ossification
GO:0009143	1.00	nucleoside triphosphate catabolic process
GO:0006091	1.00	generation of precursor metabolites and energy
GO:2000026	0.61	regulation of multicellular organismal development
GO:0030500	0.60	regulation of bone mineralization
GO:0006771	0.60	riboflavin metabolic process

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:0016020	1.00	membrane
GO:0044424	0.89	intracellular part
GO:0044425	0.86	membrane part
GO:0044444	0.85	cytoplasmic part
GO:0016021	0.85	integral component of membrane
GO:0005886	0.85	plasma membrane
GO:0005887	0.84	integral component of plasma membrane
GO:0044446	0.80	intracellular organelle part
GO:0031090	0.77	organelle membrane
GO:0005765	0.76	lysosomal membrane
GO:0044421	0.62	extracellular region part
GO:0005615	0.60	extracellular space
GO:0009986	0.59	cell surface

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	3m9uA	0.519	3.88	0.082	0.844	2.5.1.10	NA
2	0.060	1onfA	0.478	4.30	0.080	0.885	1.8.1.7	57
3	0.060	2jifA	0.507	4.20	0.105	0.927	1.3.99.-	58
4	0.060	1zczB	0.482	4.19	0.054	0.854	3.5.4.10 2.1.2.3	NA
5	0.060	2wbiB	0.516	4.13	0.057	0.885	1.3.99.-	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	2ix6B	0.524	3.83	0.093	0.885	0.26	FAD	complex1.pdb.gz	53,92,94
2	0.01	1jqiA	0.528	3.94	0.100	0.896	0.10	FAD	complex2.pdb.gz	88,90,93
3	0.01	2ebaF	0.423	4.56	0.093	0.823	0.23	FAD	complex3.pdb.gz	52,54,94
4	0.01	3pdeD	0.419	4.64	0.022	0.771	0.26	IPE	complex4.pdb.gz	41,42,47,77
5	0.01	1pbfA	0.509	4.25	0.065	0.906	0.14	BHA	complex5.pdb.gz	1,50,52,60
6	0.01	1bkwA	0.511	4.23	0.065	0.906	0.10	FAD	complex6.pdb.gz	37,38,39
7	0.01	2ix5B	0.390	4.62	0.027	0.750	0.11	CAA	complex7.pdb.gz	77,81,84
8	0.01	2ix5B	0.390	4.62	0.027	0.750	0.24	FAD	complex8.pdb.gz	56,85,86,90
9	0.01	2wbiA	0.363	3.69	0.038	0.552	0.28	FAD	complex9.pdb.gz	57,86,88
10	0.01	2ebaE	0.483	4.25	0.066	0.885	0.19	FAD	complex10.pdb.gz	56,93,96

	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.