D-I-TASSER P61812-D1

D-I-TASSER results for P61812-D1

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

Input Sequence in FASTA format

>P61812 (51 residues)
MHYCVLSAFLILHLVTVALSLSTCSTLDMDQFMRKRIEAIRGQILSKLKLT

Predicted Secondary Structure

Sequence	20 40 \| \| MHYCVLSAFLILHLVTVALSLSTCSTLDMDQFMRKRIEAIRGQILSKLKLT
Prediction	CCSHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC
Confidence	921599999999999985012557646788988999999999999985279
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MHYCVLSAFLILHLVTVALSLSTCSTLDMDQFMRKRIEAIRGQILSKLKLT
Prediction	431320231332332333432431442426424654153234422543648
	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

                   |                   |

SS
Seq

CCSHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC
MHYCVLSAFLILHLVTVALSLSTCSTLDMDQFMRKRIEAIRGQILSKLKLT

5tcxA

0.06

2.55

1.33

DEthreader

QQLLGTFFTCLVILFACEVAAGIWV--NKDQIAKDVKQFYDQALQQAVVDD

3rjrA1

0.69

0.43

12.27

1.55

HHsearch

-------------------PLSTSKTIDMELVKRKRIEAIRGQILSKLRLA

6k4jA

0.08

3.12

1.17

DEthreader

QCMLGLFFGFLLVIFAIEIAAAIWGYSHKDEVIKEVQEFYKDTYNKLKTKD

6vekA3

0.20

0.18

5.67

0.77

SPARKS-K

--GDLDSLQAEYNSLKDARISSQ-KEFAKDPNNAKRMEVLEKQIHNIER--

5xn5A1

0.04

1.98

0.89

MapAlign

AMPAAAAVEMVHTMSLVHDDLTCHVVYGEPIAVLTGDALLSLSFHHM----

1v4jA1

0.02

1.53

0.62

CEthreader

AISSLAALELYHLASLLHDDVTINFMYGDKAAVAAGDLVLVSAFHTVEEIG

3rjrA1

0.69

0.43

12.27

0.79

MUSTER

-------------------PLSTSKTIDMELVKRKRIEAIRGQILSKLRLA

3rjrA

0.69

0.43

12.27

1.34

HHsearch

-------------------PLSTSKTIDMELVKRKRIEAIRGQILSKLRLA

3rjrA1

0.69

0.43

12.27

0.61

FFAS-3D

-------------------PLSTSKTIDMELVKRKRIEAIRGQILSKLRLA

4nknA

0.06

2.59

0.50

EigenThreader

VVRQLCQESFSLGLKKLLDVTCSSLSVTQEEAEELLQALHRLVAFRDSTWR

(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	0.5692

(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	2fbwC	0.75	1.42	0.040	0.941	model1_2fbwC.pdb.gz
2	3vr8C	0.73	1.84	0.059	0.980	model1_3vr8C.pdb.gz
3	4fgwA	0.71	1.67	0.061	0.961	model1_4fgwA.pdb.gz
4	1x0xA2	0.68	1.82	0.102	0.961	model1_1x0xA2.pdb.gz
5	1z82A2	0.66	1.94	0.104	0.941	model1_1z82A2.pdb.gz
6	1yj8A2	0.62	1.91	0.043	0.922	model1_1yj8A2.pdb.gz
7	1txgA2	0.59	2.41	0.020	0.980	model1_1txgA2.pdb.gz
8	3k96A2	0.58	2.50	0.118	1.000	model1_3k96A2.pdb.gz
9	1n1eA2	0.55	2.28	0.080	0.902	model1_1n1eA2.pdb.gz
10	1guzA1	0.50	2.95	0.119	0.824	model1_1guzA1.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:0005114	1.00	type II transforming growth factor beta receptor binding
GO:0034714	0.91	type III transforming growth factor beta receptor binding
GO:0042802	0.68	identical protein binding
GO:0003824	0.51	catalytic 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:0065007	1.00	biological regulation
GO:0050789	1.00	regulation of biological process
GO:0044767	1.00	single-organism developmental process
GO:0080090	0.99	regulation of primary metabolic process
GO:0048583	0.99	regulation of response to stimulus
GO:0044763	0.99	single-organism cellular process
GO:0031325	0.99	positive regulation of cellular metabolic process
GO:0010604	0.99	positive regulation of macromolecule metabolic process
GO:0007167	0.99	enzyme linked receptor protein signaling pathway
GO:0007179	0.98	transforming growth factor beta receptor signaling pathway
GO:2000026	0.91	regulation of multicellular organismal development
GO:0048523	0.91	negative regulation of cellular process
GO:1901700	0.90	response to oxygen-containing compound
GO:0051241	0.90	negative regulation of multicellular organismal process
GO:0051240	0.90	positive regulation of multicellular organismal process
GO:0051130	0.90	positive regulation of cellular component organization
GO:0051094	0.90	positive regulation of developmental process
GO:0050776	0.90	regulation of immune response
GO:0048585	0.90	negative regulation of response to stimulus
GO:0045595	0.90	regulation of cell differentiation
GO:0033993	0.90	response to lipid
GO:0031324	0.90	negative regulation of cellular metabolic process
GO:0030278	0.90	regulation of ossification
GO:0016043	0.90	cellular component organization
GO:0014070	0.90	response to organic cyclic compound
GO:0010557	0.90	positive regulation of macromolecule biosynthetic process
GO:0009719	0.90	response to endogenous stimulus
GO:0009653	0.90	anatomical structure morphogenesis
GO:0006950	0.90	response to stress
GO:0001817	0.90	regulation of cytokine production
GO:0045778	0.89	positive regulation of ossification
GO:0045216	0.89	cell-cell junction organization
GO:0032570	0.89	response to progesterone
GO:0010936	0.89	negative regulation of macrophage cytokine production
GO:0010718	0.89	positive regulation of epithelial to mesenchymal transition
GO:0007435	0.89	salivary gland morphogenesis
GO:0044707	0.85	single-multicellular organism process
GO:0048584	0.84	positive regulation of response to stimulus
GO:0032268	0.84	regulation of cellular protein metabolic process
GO:0019220	0.84	regulation of phosphate metabolic process
GO:0010646	0.84	regulation of cell communication
GO:0048869	0.83	cellular developmental process
GO:0043408	0.83	regulation of MAPK cascade
GO:0042127	0.83	regulation of cell proliferation
GO:0009967	0.83	positive regulation of signal transduction
GO:0001934	0.83	positive regulation of protein phosphorylation
GO:0008152	0.71	metabolic process
GO:0044238	0.70	primary metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0043170	0.70	macromolecule metabolic process
GO:0032879	0.70	regulation of localization
GO:0051223	0.69	regulation of protein transport
GO:0051050	0.69	positive regulation of transport
GO:0050790	0.69	regulation of catalytic activity
GO:0048856	0.69	anatomical structure development
GO:0044765	0.69	single-organism transport
GO:0044260	0.69	cellular macromolecule metabolic process
GO:0030334	0.69	regulation of cell migration
GO:0030198	0.69	extracellular matrix organization
GO:0008285	0.69	negative regulation of cell proliferation
GO:0071822	0.68	protein complex subunit organization
GO:0051222	0.68	positive regulation of protein transport
GO:0050680	0.68	negative regulation of epithelial cell proliferation
GO:0045936	0.68	negative regulation of phosphate metabolic process
GO:0045860	0.68	positive regulation of protein kinase activity
GO:0045786	0.68	negative regulation of cell cycle
GO:0043410	0.68	positive regulation of MAPK cascade
GO:0030335	0.68	positive regulation of cell migration
GO:0030155	0.68	regulation of cell adhesion
GO:0030154	0.68	cell differentiation
GO:0022402	0.68	cell cycle process
GO:0009611	0.68	response to wounding
GO:0007184	0.68	SMAD protein import into nucleus
GO:0006468	0.68	protein phosphorylation
GO:0097191	0.67	extrinsic apoptotic signaling pathway
GO:0060389	0.67	pathway-restricted SMAD protein phosphorylation
GO:0044710	0.67	single-organism metabolic process
GO:0035303	0.67	regulation of dephosphorylation
GO:0030308	0.67	negative regulation of cell growth
GO:0010634	0.67	positive regulation of epithelial cell migration
GO:0008284	0.67	positive regulation of cell proliferation
GO:0007050	0.67	cell cycle arrest
GO:0023014	0.66	signal transduction by protein phosphorylation
GO:0042981	0.65	regulation of apoptotic process
GO:1903532	0.51	positive regulation of secretion by cell
GO:0050708	0.51	regulation of protein secretion
GO:0048513	0.51	animal organ development
GO:0016477	0.51	cell migration
GO:0050714	0.50	positive regulation of protein secretion
GO:0001837	0.50	epithelial to mesenchymal transition

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	1.00	extracellular region part
GO:0005615	0.85	extracellular space
GO:0031012	0.73	extracellular matrix
GO:0044464	0.66	cell part
GO:0005576	0.61	extracellular region
GO:0044424	0.57	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	0.335	1wu0A	0.498	2.50	0.063	0.922	3.6.3.14	38
2	0.060	2qppB	0.593	2.54	0.040	0.922	1.14.99.3	NA
3	0.060	1gpjA	0.625	1.95	0.059	0.941	1.2.1.70	NA
4	0.060	1etuA	0.442	1.96	0.070	0.627	3.6.5.3	NA
5	0.060	2ywcA	0.619	1.85	0.087	0.882	6.3.5.2	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	0.03	2plaA	0.661	1.91	0.122	0.961	0.55	PO4	complex1.pdb.gz	39,42,43,44

	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.