D-I-TASSER P28906-D3

D-I-TASSER results for P28906-D3

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

Input Sequence in FASTA format

>P28906 (108 residues)
QDVASHQSYSQKTLIALVTSGALLAVLGITGYFLMNRRSWSPTGERLGEDPYYTENGGGQ
GYSSGPGTSPEAQGKASVNRGAQENGTGQATSRNGHSARQHVVADTEL

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| QDVASHQSYSQKTLIALVTSGALLAVLGITGYFLMNRRSWSPTGERLGEDPYYTENGGGQGYSSGPGTSPEAQGKASVNRGAQENGTGQATSRNGHSARQHVVADTEL
Prediction	CHHHHHHCHCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCSSCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	803533011125679899999999999998988640346797651414686301269985364278899764567776788744688999988987766664467879
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| QDVASHQSYSQKTLIALVTSGALLAVLGITGYFLMNRRSWSPTGERLGEDPYYTENGGGQGYSSGPGTSPEAQGKASVNRGAQENGTGQATSRNGHSARQHVVADTEL
Prediction	853563653433200001332333132221121113346454544414654244645444334324444553574453556456546664446434444554346478
	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

                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHCHCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCSSCCCCCCCCCCCCCCSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
QDVASHQSYSQKTLIALVTSGALLAVLGITGYFLMNRRSWSPTGERLGEDPYYTENGGGQGYSSGPGTSPEAQGKASVNRGAQENGTGQATSRNGHSARQHVVADTEL

4am6A

0.07

3.00

0.56

CEthreader

RKPFRGGSFNVKSPYYKSLAELISDVTKLLEHALNSETLNVKPTKFNQYKVVLVIFQAVAIIQESLATCYGAGISTSTCVVNIGAAETRIACVDEGTVLEHSAITLDY

4qkwA

0.08

0.07

2.93

0.48

EigenThreader

VSALSILSLLERVSTIIDGVQASQQRMEERQQQLEGSVSAV---QSELLKLARDHGATATTVDKLLQKARRVSTHVKEVRSRV---EKQNVRVKKVETTQDELLTR--

1zrtC2

0.19

0.08

2.69

0.39

FFAS-3D

--VGAMPTEYPYDWISLIASTYWFAYFLVILPLLGATEKPEPIPASIEED----------------------------------------------------------

3bogA

0.12

0.08

2.97

0.86

SPARKS-K

---------------------------CKGADGAHGVGCPGTAGAA-GSVGGPGCDGGHGGNGGNGNPAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP--

3tt3A

0.19

0.05

1.50

0.51

CNFpred

----------FGLWIPLVVAIYYVYIESWTLGFAIKF-----------------------------------------------------------------------

6vejA

0.07

0.06

2.32

1.00

DEthreader

FGLVH--QVSN-QAQVVKKAVGGFTRALFEAVVIVLIVSFVS--LGLRAG-VV-S-A--TVMITEHKSEQKGRIAERFDSLLAMRTI-WAVLEAHHRTR--L------

4g1eB

0.10

3.75

0.92

MapAlign

LIFAVTENVVNLYQNYSELMDSSNVLQLIVDAYGKINGTFECGVCRCGPGWLGGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDW

1zzaA

0.21

0.17

5.30

0.59

MUSTER

MSIMDHSPTTGVTVIVILIAIAALGALILGCWCYLRLQRISQ-----SED---EESIVGDGETKEPFLLVQYSAKPCVERKAK---LMTPNGPEVHG-----------

2l2tA

0.19

0.07

2.39

0.58

HHsearch

---STLPQARTPLIAAGVIGGLFILVVGLTFAVYVRRKSIKKKRA---------------------------------------------------------------

5x5yG

0.08

0.07

2.94

0.52

CEthreader

TIMRAAGVSLSRIVWAVMKPMLVLMLAGILVGEYVAPWTENIAQSGRALAQGGGDSQSSKR------GLWHRQGREYIHINAVQPNGVLYGVTRYRFDEQRGLESASF

(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	0.3842

(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	3i39X	0.51	4.58	0.065	0.889	model1_3i39X.pdb.gz
2	3i04A	0.50	4.35	0.080	0.861	model1_3i04A.pdb.gz
3	6elqX	0.50	4.63	0.056	0.907	model1_6elqX.pdb.gz
4	5doqA	0.50	4.46	0.010	0.852	model1_5doqA.pdb.gz
5	3vstA	0.49	4.10	0.032	0.843	model1_3vstA.pdb.gz
6	3cf4A1	0.42	4.99	0.079	0.806	model1_3cf4A1.pdb.gz
7	4eeiA	0.41	4.48	0.032	0.732	model1_4eeiA.pdb.gz
8	2ylaA	0.40	5.10	0.095	0.796	model1_2ylaA.pdb.gz
9	1jqkA1	0.38	4.50	0.037	0.657	model1_1jqkA1.pdb.gz
10	3b40A	0.36	4.58	0.065	0.667	model1_3b40A.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:0030246	1.00	carbohydrate 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:0007160	1.00	cell-matrix adhesion
GO:0065007	0.78	biological regulation
GO:0050789	0.78	regulation of biological process
GO:0044699	0.77	single-organism process
GO:0050794	0.75	regulation of cellular process
GO:0009987	0.75	cellular process
GO:0048518	0.72	positive regulation of biological process
GO:0048522	0.70	positive regulation of cellular process
GO:0031323	0.70	regulation of cellular metabolic process
GO:0048583	0.69	regulation of response to stimulus
GO:0048523	0.69	negative regulation of cellular process
GO:0044763	0.69	single-organism cellular process
GO:0065008	0.68	regulation of biological quality
GO:0051240	0.68	positive regulation of multicellular organismal process
GO:0051171	0.68	regulation of nitrogen compound metabolic process
GO:0032501	0.68	multicellular organismal process
GO:0031326	0.68	regulation of cellular biosynthetic process
GO:1901214	0.67	regulation of neuron death
GO:0080135	0.67	regulation of cellular response to stress
GO:0060548	0.67	negative regulation of cell death
GO:0051172	0.67	negative regulation of nitrogen compound metabolic process
GO:0051094	0.67	positive regulation of developmental process
GO:0048585	0.67	negative regulation of response to stimulus
GO:0045765	0.67	regulation of angiogenesis
GO:0045597	0.67	positive regulation of cell differentiation
GO:0032733	0.67	positive regulation of interleukin-10 production
GO:0031327	0.67	negative regulation of cellular biosynthetic process
GO:0030193	0.67	regulation of blood coagulation
GO:0016337	0.67	single organismal cell-cell adhesion
GO:0008283	0.67	cell proliferation
GO:0003008	0.67	system process
GO:0001894	0.67	tissue homeostasis
GO:0001818	0.67	negative regulation of cytokine production
GO:2001214	0.66	positive regulation of vasculogenesis
GO:1901215	0.66	negative regulation of neuron death
GO:1900038	0.66	negative regulation of cellular response to hypoxia
GO:1900035	0.66	negative regulation of cellular response to heat
GO:0071636	0.66	positive regulation of transforming growth factor beta production
GO:0045766	0.66	positive regulation of angiogenesis
GO:0045019	0.66	negative regulation of nitric oxide biosynthetic process
GO:0042482	0.66	positive regulation of odontogenesis
GO:0035759	0.66	mesangial cell-matrix adhesion
GO:0032720	0.66	negative regulation of tumor necrosis factor production
GO:0030195	0.66	negative regulation of blood coagulation
GO:0008217	0.66	regulation of blood pressure
GO:0003094	0.66	glomerular filtration
GO:0060255	0.61	regulation of macromolecule metabolic process
GO:0032502	0.61	developmental process
GO:0048856	0.60	anatomical structure development
GO:0044767	0.60	single-organism developmental process
GO:0016043	0.59	cellular component organization
GO:0010468	0.59	regulation of gene expression
GO:0051049	0.58	regulation of transport
GO:0048513	0.58	animal organ development
GO:0010605	0.58	negative regulation of macromolecule metabolic process
GO:0007154	0.58	cell communication
GO:0006996	0.58	organelle organization
GO:1900041	0.57	negative regulation of interleukin-2 secretion
GO:0071971	0.57	extracellular exosome assembly
GO:0071657	0.57	positive regulation of granulocyte colony-stimulating factor production
GO:0071425	0.57	hematopoietic stem cell proliferation
GO:0038001	0.57	paracrine signaling
GO:0030097	0.57	hemopoiesis
GO:0010629	0.57	negative regulation of gene expression
GO:0001935	0.57	endothelial cell proliferation

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:0044459	1.00	plasma membrane part
GO:0044424	0.83	intracellular part
GO:0044444	0.74	cytoplasmic part
GO:0043226	0.74	organelle
GO:0016020	0.74	membrane
GO:0043229	0.73	intracellular organelle
GO:0043227	0.73	membrane-bounded organelle
GO:0043231	0.72	intracellular membrane-bounded organelle
GO:0032991	0.70	macromolecular complex
GO:0005886	0.70	plasma membrane
GO:0044421	0.69	extracellular region part
GO:0043234	0.69	protein complex
GO:0005773	0.68	vacuole
GO:0098796	0.67	membrane protein complex
GO:0098590	0.67	plasma membrane region
GO:0048471	0.67	perinuclear region of cytoplasm
GO:0005764	0.67	lysosome
GO:0005737	0.67	cytoplasm
GO:0045171	0.66	intercellular bridge
GO:0036053	0.66	glomerular endothelium fenestra
GO:0016324	0.66	apical plasma membrane
GO:0009925	0.66	basal plasma membrane
GO:0009897	0.66	external side of plasma membrane
GO:0031224	0.65	intrinsic component of membrane
GO:0016021	0.64	integral component of membrane
GO:0005887	0.63	integral component of plasma membrane

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	1qh4A	0.469	4.39	0.064	0.815	2.7.3.2	NA
2	0.060	2wpnB	0.446	4.20	0.030	0.768	1.12.7.2	NA
3	0.060	1u6rA	0.472	4.56	0.052	0.824	2.7.3.2	NA
4	0.060	1asyA	0.444	5.07	0.040	0.843	6.1.1.12	NA
5	0.060	3b8eC	0.455	4.80	0.087	0.861	3.6.3.9	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	1e3dB	0.466	4.21	0.052	0.787	0.51	H2S	complex1.pdb.gz	54,57,60

	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.