D-I-TASSER P42229-D3

D-I-TASSER results for P42229-D3

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

Input Sequence in FASTA format

>P42229 (50 residues)
EYFIIQYQESLRIQAQFAQLAQLSPQERLSRETALQQKQVSLEAWLQREA

Predicted Secondary Structure

Sequence	20 40 \| \| EYFIIQYQESLRIQAQFAQLAQLSPQERLSRETALQQKQVSLEAWLQREA
Prediction	CSSSSSHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	92554204567799999988609946653455799999999999997309
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| EYFIIQYQESLRIQAQFAQLAQLSPQERLSRETALQQKQVSLEAWLQREA
Prediction	83222423652414341452471546644565442554544144225568
	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

                   |                   |

SS
Seq

CSSSSSHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCC
EYFIIQYQESLRIQAQFAQLAQLSPQERLSRETALQQKQVSLEAWLQREA

3g67A

0.10

3.70

1.50

DEthreader

ETLENIRSIEKLIQNIMRIARETVQNLSNETNEVTKQIVEKAREILESSQ

1y1uA1

0.91

0.86

24.16

1.27

SPARKS-K

-YFIIQYQESLRIQAQFAQLGQLNPQERMSRETALQQKQVSLETWLQR--

1y1uA1

0.91

0.86

24.16

2.00

HHsearch

-YFIIQYQESLRIQAQFAQLGQLNPQERMSRETALQQKQVSLETWLQR--

5owvA

0.16

5.32

1.50

DEthreader

ALRAYKKELHLELKNILSEYEQNSFEENLEKIEKLKQLEMGLLNADKLHH

7apkG2

0.13

0.12

4.18

1.00

SPARKS-K

---HETLKELEALGKELEHLSHIKESVEDKLELRRKQFHVLLSTIHELQQ

6yvuA

0.06

2.62

0.82

MapAlign

AQLAKAKTELNEVSLAIKKSSMKMIGECENEIKTKQMSLKKCQEEVSTIE

6vq6g

0.04

2.08

0.59

CEthreader

GASSAMVFSAMGAAYGTAKSGTGIIMKSIIPVVMAGIIAIYGLVVAVLIA

1y1uA

0.92

25.84

0.89

MUSTER

EYFIIQYQESLRIQAQFAQLGQLNPQERMSRETALQQKQVSLETWLQREA

1y1uA

0.92

25.84

1.27

HHsearch

EYFIIQYQESLRIQAQFAQLGQLNPQERMSRETALQQKQVSLETWLQREA

1y1uA1

0.91

0.86

24.16

0.97

FFAS-3D

-YFIIQYQESLRIQAQFAQLGQLNPQERMSRETALQQKQVSLETWLQR--

(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	0.7371

(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	1l8dA	0.90	0.96	0.060	1.000	model1_1l8dA.pdb.gz
2	4abmA	0.89	1.16	0.060	1.000	model1_4abmA.pdb.gz
3	6dmpA	0.89	1.04	0.160	1.000	model1_6dmpA.pdb.gz
4	2gscB	0.88	0.92	0.100	1.000	model1_2gscB.pdb.gz
5	4hwdD	0.88	1.20	0.100	1.000	model1_4hwdD.pdb.gz
6	4hwiB	0.87	1.34	0.100	1.000	model1_4hwiB.pdb.gz
7	4wheA2	0.87	1.03	0.080	1.000	model1_4wheA2.pdb.gz
8	6gczA	0.87	0.97	0.120	1.000	model1_6gczA.pdb.gz
9	4hwhA	0.87	1.21	0.120	1.000	model1_4hwhA.pdb.gz
10	5vykA1	0.87	1.05	0.080	1.000	model1_5vykA1.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:1901363	0.85	heterocyclic compound binding
GO:0097159	0.85	organic cyclic compound binding
GO:0003676	0.83	nucleic acid binding
GO:0003677	0.82	DNA binding
GO:0004871	0.57	signal transducer 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:0044699	1.00	single-organism process
GO:0009987	1.00	cellular process
GO:0007259	1.00	JAK-STAT cascade
GO:0006355	1.00	regulation of transcription, DNA-templated
GO:0048522	0.95	positive regulation of cellular process
GO:0051240	0.94	positive regulation of multicellular organismal process
GO:0050793	0.94	regulation of developmental process
GO:0006357	0.94	regulation of transcription from RNA polymerase II promoter
GO:0044763	0.89	single-organism cellular process
GO:0031325	0.88	positive regulation of cellular metabolic process
GO:0010604	0.88	positive regulation of macromolecule metabolic process
GO:1903708	0.87	positive regulation of hemopoiesis
GO:0045944	0.87	positive regulation of transcription from RNA polymerase II promoter
GO:0045637	0.87	regulation of myeloid cell differentiation
GO:0045597	0.87	positive regulation of cell differentiation
GO:0019221	0.83	cytokine-mediated signaling pathway
GO:0032502	0.82	developmental process
GO:0065008	0.76	regulation of biological quality
GO:0002376	0.75	immune system process
GO:0045321	0.74	leukocyte activation
GO:0030154	0.74	cell differentiation
GO:0038161	0.73	prolactin signaling pathway
GO:0030098	0.73	lymphocyte differentiation
GO:0045646	0.69	regulation of erythrocyte differentiation
GO:0040014	0.69	regulation of multicellular organism growth
GO:0022414	0.69	reproductive process
GO:0008284	0.69	positive regulation of cell proliferation
GO:0008152	0.68	metabolic process
GO:0071704	0.67	organic substance metabolic process
GO:0044238	0.67	primary metabolic process
GO:0044237	0.67	cellular metabolic process
GO:1901360	0.65	organic cyclic compound metabolic process
GO:0051179	0.63	localization
GO:0048856	0.60	anatomical structure development
GO:0044767	0.60	single-organism developmental process
GO:0051246	0.59	regulation of protein metabolic process
GO:0048583	0.59	regulation of response to stimulus
GO:0048523	0.59	negative regulation of cellular process
GO:0051247	0.57	positive regulation of protein metabolic process
GO:0048584	0.57	positive regulation of response to stimulus
GO:0045639	0.57	positive regulation of myeloid cell differentiation
GO:0043067	0.57	regulation of programmed cell death
GO:0001819	0.57	positive regulation of cytokine production
GO:1902107	0.56	positive regulation of leukocyte differentiation
GO:0051241	0.56	negative regulation of multicellular organismal process
GO:0051093	0.56	negative regulation of developmental process
GO:0050870	0.56	positive regulation of T cell activation
GO:0050671	0.56	positive regulation of lymphocyte proliferation
GO:0045619	0.56	regulation of lymphocyte differentiation
GO:0043066	0.56	negative regulation of apoptotic process
GO:0042592	0.56	homeostatic process
GO:0032101	0.56	regulation of response to external stimulus
GO:0031349	0.56	positive regulation of defense response
GO:0030101	0.56	natural killer cell activation
GO:0019216	0.56	regulation of lipid metabolic process
GO:0007346	0.56	regulation of mitotic cell cycle
GO:0003006	0.56	developmental process involved in reproduction
GO:0002683	0.56	negative regulation of immune system process
GO:0050729	0.55	positive regulation of inflammatory response
GO:0046543	0.55	development of secondary female sexual characteristics
GO:0045931	0.55	positive regulation of mitotic cell cycle
GO:0045647	0.55	negative regulation of erythrocyte differentiation
GO:0045579	0.55	positive regulation of B cell differentiation
GO:0045086	0.55	positive regulation of interleukin-2 biosynthetic process
GO:0043029	0.55	T cell homeostasis
GO:0042104	0.55	positive regulation of activated T cell proliferation
GO:0040018	0.55	positive regulation of multicellular organism growth
GO:0032501	0.55	multicellular organismal process
GO:0030856	0.55	regulation of epithelial cell differentiation
GO:0019915	0.55	lipid storage
GO:0019218	0.55	regulation of steroid metabolic process
GO:0001779	0.55	natural killer cell differentiation
GO:0044707	0.54	single-multicellular organism process
GO:0044702	0.54	single organism reproductive process
GO:0006810	0.54	transport
GO:0007595	0.53	lactation
GO:0001553	0.53	luteinization
GO:0050896	0.52	response to stimulus
GO:0044281	0.51	small molecule metabolic process
GO:0006629	0.50	lipid 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:0005737	1.00	cytoplasm
GO:0043226	0.79	organelle
GO:0043229	0.78	intracellular organelle
GO:0043227	0.78	membrane-bounded organelle
GO:0043231	0.77	intracellular membrane-bounded organelle
GO:0005634	0.76	nucleus
GO:0044446	0.55	intracellular organelle part
GO:0044444	0.55	cytoplasmic part
GO:0044428	0.50	nuclear 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	0.351	2w5jA	0.650	2.11	0.102	0.980	3.6.3.14	43
2	0.316	2wieA	0.656	2.08	0.102	0.980	3.6.3.14	43
3	0.067	3eabA	0.762	1.96	0.080	1.000	3.6.4.3	NA
4	0.067	1z8yM	0.471	1.61	0.032	0.560	3.4.21.90	NA
5	0.066	2k9yA	0.525	1.86	0.083	0.720	2.7.10.1	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:

No Binding sites was predicted

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

	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.