D-I-TASSER P55008-D1

D-I-TASSER results for P55008-D1

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

Input Sequence in FASTA format

>P55008 (147 residues)
MSQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLN
GNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKM
ILMYEEKAREKEKPTGPPAKKAISELP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPAKKAISELP
Prediction	CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Confidence	997543202678877889999999999875035212321027999999999999997689999717999999999919999999999999998378998053999999999745789999999864067877888999964211288
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPAKKAISELP
Prediction	876564361044144135624641463265216475156564266315403610530064552403262045046514461356204520540063561403172034103443641241141145456657555444464426728
	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                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCSCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
MSQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPAKKAISELP

2g2bA

0.96

0.77

21.56

1.00

DEthreader

-----DL-QGGAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMI---------------------Y--EE

2g2bA

0.99

27.82

1.24

SPARKS-K

ESQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPAKKAISELP

2g2bA

0.84

0.74

20.90

0.68

MapAlign

-------QGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRILKMILMYEEKAREKEKPTGPP-----------

2g2bA

0.99

27.82

0.49

CEthreader

ESQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPAKKAISELP

2g2bA

0.99

27.82

1.53

MUSTER

ESQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPAKKAISELP

2g2bA

0.99

27.63

0.93

HHsearch

ESQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEV-SGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPAKKAISELP

2g2bA

1.00

0.99

27.81

1.96

FFAS-3D

-SQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPAKKAISELP

1y1xA

0.10

3.74

0.85

EigenThreader

ARHMNDNQELMEWFRAVDNAALSSAATTEKLLHMYDKNHSGEITHFILSMREGFRKRDSSGDGRLDSNEVRAALLSSGYQVSEQTFQALMRKFDRQRRGSLGFDDYVELSIFVCRVRNVFAFYDRE--RTGQVTFTFDTFIGGSVSI

2g2bA

0.99

27.82

1.15

CNFpred

ESQTRDLQGGKAFGLLKAQQEERLDEINKQFLDDPKYSSDEDLPSKLEGFKEKYMEFDLNGNGDIDIMSLKRMLEKLGVPKTHLELKKLIGEVSSGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREKEKPTGPPAKKAISELP

2jjzC

0.63

0.48

13.81

1.00

DEthreader

---------KA-FGLLKARQERRLAEINREFLCDQKYSDEENLPEKLTAFKEKYMEFDLNNEGEIDLMSLKRMMEKLGVPKTHLEMKKMISEVTGVSD-TISYRDFVNMMLGK-RSAVLKL--V-----------------MF--E-

(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	0.634

(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	2g2bA	0.87	1.09	0.905	0.912	model1_2g2bA.pdb.gz
2	2jjzC	0.68	2.08	0.652	0.775	model1_2jjzC.pdb.gz
3	5i2lA	0.52	2.75	0.265	0.646	model1_5i2lA.pdb.gz
4	7bvcA	0.52	4.55	0.059	0.816	model1_7bvcA.pdb.gz
5	2f2pA	0.51	3.25	0.150	0.653	model1_2f2pA.pdb.gz
6	4n5xA	0.51	3.03	0.126	0.646	model1_4n5xA.pdb.gz
7	2xqoA	0.50	4.00	0.087	0.748	model1_2xqoA.pdb.gz
8	1xfyO	0.46	2.76	0.236	0.558	model1_1xfyO.pdb.gz
9	1dguA	0.46	3.45	0.087	0.612	model1_1dguA.pdb.gz
10	1dtlA1	0.44	2.74	0.275	0.531	model1_1dtlA1.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:0008092	0.76	cytoskeletal protein binding
GO:0032403	0.75	protein complex binding
GO:0051015	0.72	actin filament 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:0065007	0.94	biological regulation
GO:0050789	0.93	regulation of biological process
GO:0009987	0.89	cellular process
GO:0044699	0.86	single-organism process
GO:0050794	0.84	regulation of cellular process
GO:0044763	0.83	single-organism cellular process
GO:0050896	0.81	response to stimulus
GO:0016043	0.80	cellular component organization
GO:0048518	0.78	positive regulation of biological process
GO:0007165	0.77	signal transduction
GO:0048583	0.76	regulation of response to stimulus
GO:0042221	0.76	response to chemical
GO:0048522	0.75	positive regulation of cellular process
GO:0022607	0.75	cellular component assembly
GO:0051726	0.74	regulation of cell cycle
GO:0051716	0.74	cellular response to stimulus
GO:0048584	0.74	positive regulation of response to stimulus
GO:0035556	0.74	intracellular signal transduction
GO:0032879	0.74	regulation of localization
GO:0006950	0.74	response to stress
GO:0032101	0.73	regulation of response to external stimulus
GO:0030030	0.73	cell projection organization
GO:0010564	0.73	regulation of cell cycle process
GO:0010033	0.73	response to organic substance
GO:0002682	0.73	regulation of immune system process
GO:0043933	0.72	macromolecular complex subunit organization
GO:0030031	0.72	cell projection assembly
GO:0071822	0.71	protein complex subunit organization
GO:0071310	0.71	cellular response to organic substance
GO:0061024	0.71	membrane organization
GO:0051270	0.71	regulation of cellular component movement
GO:0051017	0.71	actin filament bundle assembly
GO:0050921	0.71	positive regulation of chemotaxis
GO:0034622	0.71	cellular macromolecular complex assembly
GO:0008284	0.71	positive regulation of cell proliferation
GO:0007346	0.71	regulation of mitotic cell cycle
GO:0006952	0.71	defense response
GO:0002684	0.71	positive regulation of immune system process
GO:2000406	0.70	positive regulation of T cell migration
GO:1900087	0.70	positive regulation of G1/S transition of mitotic cell cycle
GO:0097178	0.70	ruffle assembly
GO:0090026	0.70	positive regulation of monocyte chemotaxis
GO:0071673	0.70	positive regulation of smooth muscle cell chemotaxis
GO:0071346	0.70	cellular response to interferon-gamma
GO:0048661	0.70	positive regulation of smooth muscle cell proliferation
GO:0042102	0.70	positive regulation of T cell proliferation
GO:0030041	0.70	actin filament polymerization
GO:0016601	0.70	Rac protein signal transduction
GO:0006954	0.70	inflammatory response
GO:0006911	0.70	phagocytosis, engulfment

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:0044464	0.98	cell part
GO:0044424	0.96	intracellular part
GO:0044446	0.89	intracellular organelle part
GO:0044444	0.88	cytoplasmic part
GO:0044430	0.84	cytoskeletal part
GO:0043226	0.82	organelle
GO:0043229	0.80	intracellular organelle
GO:0043227	0.76	membrane-bounded organelle
GO:0016020	0.74	membrane
GO:0005829	0.72	cytosol
GO:0043231	0.70	intracellular membrane-bounded organelle
GO:0099513	0.68	polymeric cytoskeletal fiber
GO:0005884	0.67	actin filament
GO:0044425	0.66	membrane part
GO:0005634	0.66	nucleus
GO:0042995	0.64	cell projection
GO:0005737	0.64	cytoplasm
GO:0044463	0.63	cell projection part
GO:0044459	0.62	plasma membrane part
GO:0032587	0.60	ruffle membrane
GO:0030027	0.60	lamellipodium
GO:0001891	0.60	phagocytic cup

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	2eabA	0.443	5.06	0.063	0.782	3.2.1.63	NA
2	0.060	2weiA	0.337	5.35	0.008	0.633	2.7.1.17	NA
3	0.060	1cpoA	0.453	4.58	0.054	0.748	1.11.1.10	NA
4	0.060	1z11A	0.448	3.67	0.051	0.612	1.14.14.1	NA
5	0.060	2uv8G	0.469	4.73	0.052	0.762	2.3.1.86	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.54	2kn2A	0.499	2.26	0.227	0.585	1.13	CA	complex1.pdb.gz	60,62,64,69
2	0.35	1wy9A	0.550	3.01	0.736	0.714	1.64	CA	complex2.pdb.gz	90,94,96,97,100,105
3	0.02	1y1xA	0.473	4.19	0.100	0.680	1.13	CA	complex3.pdb.gz	91,95,97,99
4	0.01	1o9kB	0.451	3.19	0.033	0.605	0.97	III	complex4.pdb.gz	45,46,49,52,53

	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.