D-I-TASSER P19474-D2

D-I-TASSER results for P19474-D2

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

Input Sequence in FASTA format

>P19474 (39 residues)
ERCAVHGERLHLFCEKDGKALCWVCAQSRKHRDHAMVPL

Predicted Secondary Structure

Sequence	20 \| ERCAVHGERLHLFCEKDGKALCWVCAQSRKHRDHAMVPL
Prediction	CCCHHHCCSSSSSSCCCCSSSSSSCCCCCCCCCCCSSSC
Confidence	944432963234543389478847256743489807629
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 \| ERCAVHGERLHLFCEKDGKALCWVCAQSRKHRDHAMVPL
Prediction	842761754043005526420010054176167144347
	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

                   |

SS
Seq

CCCHHHCCSSSSSSCCCCSSSSSSCCCCCCCCCCCSSSC
ERCAVHGERLHLFCEKDGKALCWVCAQSRKHRDHAMVPL

3vk6A

0.03

1.67

1.00

DEthreader

VH-FGLPIKVYGRMIPCKHVFCYCAILHKDKMPVRIEQC

5jpxA

1.00

28.00

3.87

SPARKS-K

ERCAVHGERLHLFCEKDGKALCWVCAQSRKHRDHAMVPL

5va4A

0.46

13.46

0.89

MapAlign

DHCAHHGEKLVLFCQQDGNVICWLCERSQEHRGHQTFLV

5va4A

0.46

13.46

0.70

CEthreader

DHCAHHGEKLVLFCQQDGNVICWLCERSQEHRGHQTFLV

5olmA

1.00

28.00

1.85

MUSTER

ERCAVHGERLHLFCEKDGKALCWVCAQSRKHRDHAMVPL

5va4A

0.46

13.46

1.66

HHsearch

DHCAHHGEKLVLFCQQDGNVICWLCERSQEHRGHQTFLV

5olmA2

1.00

28.00

0.68

FFAS-3D

ERCAVHGERLHLFCEKDGKALCWVCAQSRKHRDHAMVPL

3dznA

0.08

3.08

0.47

EigenThreader

PPTTIKGFNVDFSPTGCRGVRCAGCYCCCGPTSSNYRVT

5eiuA

0.46

13.46

1.42

CNFpred

DHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLM

2egmA

0.49

0.46

13.41

1.00

DEthreader

GICPQE--ALKLFCEVDEEAICVVCRESRSHKQHSVVPL

(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	0.7676

(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	2egmA	0.91	0.57	0.513	1.000	model1_2egmA.pdb.gz
2	5olmA	0.91	0.61	1.000	1.000	model1_5olmA.pdb.gz
3	5va4A	0.88	0.71	0.462	1.000	model1_5va4A.pdb.gz
4	2yrgA	0.88	0.70	0.513	1.000	model1_2yrgA.pdb.gz
5	2yvrA	0.87	0.72	0.395	0.974	model1_2yvrA.pdb.gz
6	2csvA	0.84	0.88	0.342	0.974	model1_2csvA.pdb.gz
7	4tn3A	0.84	0.91	0.462	1.000	model1_4tn3A.pdb.gz
8	2difA	0.78	0.93	0.486	0.949	model1_2difA.pdb.gz
9	2djaA	0.78	1.38	0.308	1.000	model1_2djaA.pdb.gz
10	2junA	0.69	1.34	0.282	0.974	model1_2junA.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:0003824	0.82	catalytic activity
GO:0016740	0.80	transferase activity
GO:0004842	0.79	ubiquitin-protein transferase activity
GO:0004871	0.62	signal transducer activity
GO:0004872	0.59	receptor activity
GO:0038023	0.58	signaling receptor activity
GO:0008329	0.56	signaling pattern recognition receptor 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	0.98	biological regulation
GO:0050789	0.98	regulation of biological process
GO:0050794	0.96	regulation of cellular process
GO:0048518	0.91	positive regulation of biological process
GO:0009987	0.91	cellular process
GO:0080090	0.89	regulation of primary metabolic process
GO:0060255	0.89	regulation of macromolecule metabolic process
GO:0031323	0.89	regulation of cellular metabolic process
GO:0010468	0.84	regulation of gene expression
GO:0008152	0.83	metabolic process
GO:0071704	0.82	organic substance metabolic process
GO:0065009	0.82	regulation of molecular function
GO:0044238	0.82	primary metabolic process
GO:0044237	0.82	cellular metabolic process
GO:0006355	0.82	regulation of transcription, DNA-templated
GO:0048522	0.81	positive regulation of cellular process
GO:0044260	0.81	cellular macromolecule metabolic process
GO:0043900	0.80	regulation of multi-organism process
GO:0044093	0.79	positive regulation of molecular function
GO:0051090	0.78	regulation of sequence-specific DNA binding transcription factor activity
GO:0019538	0.78	protein metabolic process
GO:0006464	0.77	cellular protein modification process
GO:0070647	0.76	protein modification by small protein conjugation or removal
GO:0051091	0.76	positive regulation of sequence-specific DNA binding transcription factor activity
GO:0016567	0.75	protein ubiquitination
GO:0048583	0.73	regulation of response to stimulus
GO:0051246	0.72	regulation of protein metabolic process
GO:0002376	0.72	immune system process
GO:0031399	0.70	regulation of protein modification process
GO:0009966	0.69	regulation of signal transduction
GO:0000209	0.67	protein polyubiquitination
GO:0009967	0.65	positive regulation of signal transduction
GO:0002682	0.64	regulation of immune system process
GO:0050776	0.61	regulation of immune response
GO:1902531	0.60	regulation of intracellular signal transduction
GO:0031347	0.60	regulation of defense response
GO:0051092	0.59	positive regulation of NF-kappaB transcription factor activity
GO:1902533	0.58	positive regulation of intracellular signal transduction
GO:0045088	0.58	regulation of innate immune response
GO:0032101	0.58	regulation of response to external stimulus
GO:0010604	0.58	positive regulation of macromolecule metabolic process
GO:0002831	0.58	regulation of response to biotic stimulus
GO:0001932	0.58	regulation of protein phosphorylation
GO:0051247	0.57	positive regulation of protein metabolic process
GO:0043122	0.57	regulation of I-kappaB kinase/NF-kappaB signaling
GO:0043123	0.56	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0031349	0.56	positive regulation of defense response
GO:0031325	0.56	positive regulation of cellular metabolic process
GO:0002684	0.56	positive regulation of immune system process
GO:0045089	0.55	positive regulation of innate immune response
GO:0031401	0.55	positive regulation of protein modification process
GO:0070534	0.54	protein K63-linked ubiquitination
GO:0001934	0.54	positive regulation of protein phosphorylation
GO:0043410	0.51	positive regulation of MAPK cascade
GO:0031664	0.51	regulation of lipopolysaccharide-mediated signaling pathway
GO:0002218	0.51	activation of innate immune response

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:0043229	0.90	intracellular organelle
GO:0044444	0.84	cytoplasmic part
GO:0032991	0.74	macromolecular complex
GO:0043232	0.67	intracellular non-membrane-bounded organelle
GO:0030529	0.62	intracellular ribonucleoprotein complex
GO:0000932	0.57	cytoplasmic mRNA processing body
GO:0043227	0.54	membrane-bounded organelle
GO:0043231	0.52	intracellular membrane-bounded organelle
GO:0005737	0.50	cytoplasm

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	0.066	3eb6A	0.613	1.80	0.184	0.949	6.3.2.19	NA
2	0.060	1b12A	0.470	2.99	0.051	0.949	3.4.21.89	NA
3	0.060	3b9jJ	0.304	3.42	0.071	0.692	1.17.1.4 1.17.3.2	NA
4	0.060	3cr8A	0.515	2.74	0.114	0.897	2.7.1.25	NA
5	0.060	1mosA	0.365	3.39	0.026	0.821	2.6.1.16	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.