D-I-TASSER O15169-D3

D-I-TASSER results for O15169-D3

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

Input Sequence in FASTA format

>O15169 (61 residues)
PATSANDSEQQSLSSDADTLSLTDSSVDGIPPYRIRKQHRREMQESVQVNGRVPLPHIPR
T

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| PATSANDSEQQSLSSDADTLSLTDSSVDGIPPYRIRKQHRREMQESVQVNGRVPLPHIPRT
Prediction	CCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Confidence	9875320666521577764412245667878313458999999999997188779999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| PATSANDSEQQSLSSDADTLSLTDSSVDGIPPYRIRKQHRREMQESVQVNGRVPLPHIPRT
Prediction	8665465444544444643241444325334446345534543453254445142443468
	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

                   |                   |                   |

SS
Seq

CCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCC
PATSANDSEQQSLSSDADTLSLTDSSVDGIPPYRIRKQHRREMQESVQVNGRVPLPHIPRT

2wzkA3

0.08

3.21

1.33

DEthreader

IYRNFEKAYLDSTERFYRTQAPSLQQNGVQNYMKYADAKLKEEEKRALRYLEVALMECNVF

2vqdA2

0.05

2.33

0.52

CEthreader

PLPEDEETALAIAREVGYPVIIKAAGGRGMRVVYELIKSAKLTRTEAGAAFGNPMVYLEKF

4orkA2

0.05

2.33

0.50

EigenThreader

IESFMERLNATLCHNDFCDFIYLLEEIGTNFGEDILRMYGYYPIETIVYGIFIENGRKEIY

5yfpE6

0.21

0.20

6.23

0.29

FFAS-3D

--TVNYDKEINKLDKYKEKLSTTASDIDNSPNSPAAHLYILEILKIMFLGIVDSYMEI---

6rawA

0.08

3.21

0.86

SPARKS-K

EENIPAFETIFYDSEGEDSGAGESDQEDQAEQRILKQRARRQWESERDRIMFEYTQFSYYG

6b19A

0.14

0.03

1.11

0.67

CNFpred

TNTTNQKTQLQAIY-----------------------------------------------

4l8tA2

0.05

2.33

1.33

DEthreader

DPELVRQAVKQLFFLIGAVTLSLFKDMCSCRKGMQIRCNISYLEEWLKDKNLQSLAKLESA

6i0yO

0.07

2.74

0.84

MapAlign

ARIRRATRARRKLQELGATRLVVHRTPRHIYAYTGKDAAAAVGKAVAERADAAREAGLQ--

3bg7A2

0.17

0.15

4.85

0.65

MUSTER

------STELIDSVKSDMTIRGTPGELTGASTNKHPDWWNEKVKNHMMQHQEDPLP-IPF-

1vt4I3

0.23

0.20

6.16

0.50

HHsearch

--------EYALHRSDHYNIPKTFDSDDLIPPYLDQSHIGHHLKNRMTLFRMV-FLDFIRH

(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	0.5476

(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	2wzkA	0.73	2.72	0.082	1.000	model1_2wzkA.pdb.gz
2	4ap2B2	0.70	2.61	0.067	0.984	model1_4ap2B2.pdb.gz
3	1ldjA	0.70	2.69	0.115	1.000	model1_1ldjA.pdb.gz
4	6wcqD2	0.70	2.77	0.115	1.000	model1_6wcqD2.pdb.gz
5	6v9iC	0.69	2.71	0.067	0.984	model1_6v9iC.pdb.gz
6	6hwjA	0.67	2.60	0.051	0.967	model1_6hwjA.pdb.gz
7	5n4wA	0.66	2.70	0.000	0.984	model1_5n4wA.pdb.gz
8	5lilA	0.66	2.47	0.085	0.951	model1_5lilA.pdb.gz
9	5iz2B	0.66	2.69	0.069	0.951	model1_5iz2B.pdb.gz
10	3fhnA	0.66	2.30	0.086	0.934	model1_3fhnA.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:0005096	0.92	GTPase activator activity
GO:0019899	0.91	enzyme binding
GO:0070016	0.90	armadillo repeat domain binding
GO:0019901	0.90	protein kinase binding
GO:0008013	0.90	beta-catenin 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:0009966	1.00	regulation of signal transduction
GO:0080090	0.98	regulation of primary metabolic process
GO:0060255	0.98	regulation of macromolecule metabolic process
GO:0031323	0.98	regulation of cellular metabolic process
GO:0030111	0.97	regulation of Wnt signaling pathway
GO:0009987	0.97	cellular process
GO:0044699	0.96	single-organism process
GO:0090244	0.95	Wnt signaling pathway involved in somitogenesis
GO:0090090	0.95	negative regulation of canonical Wnt signaling pathway
GO:0071407	0.95	cellular response to organic cyclic compound
GO:0044707	0.95	single-multicellular organism process
GO:0035412	0.95	regulation of catenin import into nucleus
GO:0006355	0.95	regulation of transcription, DNA-templated
GO:0048869	0.93	cellular developmental process
GO:0045596	0.93	negative regulation of cell differentiation
GO:0009950	0.93	dorsal/ventral axis specification
GO:0008219	0.93	cell death
GO:0048518	0.71	positive regulation of biological process
GO:0048522	0.70	positive regulation of cellular process
GO:0031325	0.69	positive regulation of cellular metabolic process
GO:0010604	0.69	positive regulation of macromolecule metabolic process
GO:0001932	0.68	regulation of protein phosphorylation
GO:0001934	0.67	positive regulation of protein phosphorylation
GO:0044767	0.65	single-organism developmental process
GO:0080135	0.64	regulation of cellular response to stress
GO:0016043	0.63	cellular component organization
GO:0009653	0.63	anatomical structure morphogenesis
GO:0009967	0.62	positive regulation of signal transduction
GO:0006996	0.62	organelle organization
GO:0048856	0.61	anatomical structure development
GO:0009887	0.61	organ morphogenesis
GO:1902531	0.60	regulation of intracellular signal transduction
GO:0065009	0.60	regulation of molecular function
GO:0003002	0.60	regionalization
GO:0048646	0.59	anatomical structure formation involved in morphogenesis
GO:0046330	0.59	positive regulation of JNK cascade
GO:0045860	0.59	positive regulation of protein kinase activity
GO:0009952	0.58	anterior/posterior pattern specification
GO:0031324	0.57	negative regulation of cellular metabolic process
GO:0010605	0.57	negative regulation of macromolecule metabolic process
GO:0060823	0.56	canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation
GO:0055001	0.56	muscle cell development
GO:0048320	0.56	axial mesoderm formation
GO:0048048	0.56	embryonic eye morphogenesis
GO:0045599	0.56	negative regulation of fat cell differentiation
GO:0034244	0.56	negative regulation of transcription elongation from RNA polymerase II promoter
GO:0031122	0.56	cytoplasmic microtubule organization
GO:0030910	0.56	olfactory placode formation
GO:0021881	0.56	Wnt-activated signaling pathway involved in forebrain neuron fate commitment
GO:0021797	0.56	forebrain anterior/posterior pattern specification
GO:0007368	0.56	determination of left/right symmetry
GO:0007257	0.56	activation of JUN kinase activity
GO:0001743	0.56	optic placode formation
GO:0060272	0.52	embryonic skeletal joint morphogenesis

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:0005737	0.98	cytoplasm
GO:0044444	0.97	cytoplasmic part
GO:0043226	0.97	organelle
GO:0043227	0.96	membrane-bounded organelle
GO:0043231	0.95	intracellular membrane-bounded organelle
GO:0044430	0.94	cytoskeletal part
GO:0043232	0.94	intracellular non-membrane-bounded organelle
GO:0031410	0.93	cytoplasmic vesicle
GO:0043234	0.92	protein complex
GO:0030877	0.91	beta-catenin destruction complex
GO:0016023	0.91	cytoplasmic, membrane-bounded vesicle
GO:0014069	0.91	postsynaptic density
GO:0005938	0.91	cell cortex
GO:0005886	0.91	plasma membrane
GO:0005881	0.91	cytoplasmic microtubule

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	1k30A	0.580	2.53	0.000	0.754	2.3.1.15	24
2	0.060	1lufA	0.583	3.07	0.088	0.918	2.7.10.1	NA
3	0.060	2bq1I	0.621	3.18	0.067	0.934	1.17.4.1	NA
4	0.060	3h9rA	0.604	3.32	0.121	0.934	2.7.11.30	NA
5	0.060	3lliA	0.574	3.24	0.033	0.951	1.8.3.2	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	0.01	3mtfA	0.592	3.13	0.100	0.951	0.10	A3F	complex1.pdb.gz	20,24,26,27,29,30

	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.