D-I-TASSER P04440-D1

D-I-TASSER results for P04440-D1

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

Input Sequence in FASTA format

>P04440 (116 residues)
MMVLQVSAAPRTVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQRFLERYIYN
REEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPM

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MMVLQVSAAPRTVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQRFLERYIYNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPM
Prediction	CCSSSCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHSSSSSSSSSSSCCCSSSSSSSSSCCSSSSSSSCCCCSSSSCCCCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCC
Confidence	93355278536999999999807722206689802325663355555784233210132541566771577657722888873256653787999999864311013674447999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MMVLQVSAAPRTVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQRFLERYIYNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPM
Prediction	73103134332111130001001233332453363013113230213321422042212332130101032342222143334406322434430453323111201221334558
	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

CCSSSCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHSSSSSSSSSSSCCCSSSSSSSSSCCSSSSSSSCCCCSSSSCCCCCCCCHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCC
MMVLQVSAAPRTVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQRFLERYIYNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPM

6kvmB1

0.45

0.34

9.82

1.00

DEthreader

---------------------------RPSA--FF-FCGAISECHYLNERVRYLQRYIYNRQQYAHFDSDVGKFVADSPLGEPQAEYWNSNAELLENRMNEVDRFCRHNYGESTVQ

1lnuB1

0.50

0.48

14.01

4.27

SPARKS-K

---FEAQKAKANKAVDGGGGSLVPRGSGGGGSERHFVYQFMGECYFTNGTQRYVTRYIYNREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETH

4s0uC

0.16

5.14

0.68

MapAlign

------AWKAQNPVLREVVDILTEQLLDIQLENYTPTLQARMSCEQKEGHSSGSWQFSIDGQTFLLFDSEKRMWTTVHPGARKMKEKWENDKDVAMSFHYISMGDCIGWLEDFLMG

1kcgC

0.18

5.89

0.54

CEthreader

HLEEQLYATDAWGKQLEMLREVGQRLRLELADTEPLTLQVRMSCECEDGYIRGSWQFSFDGRKFLLFDSNNRKWTVVHAGARRMKEKWEKDSGLTTFFKMVSMRDCKSWLRDFLMH

3lqzB1

0.82

0.71

19.95

3.06

MUSTER

----------------RKFHYLPFLPSTGGSSPENYLFQGRQECYAFNGTQRFLERYIYNREEFVRFDSDVGEFRAVTELGRPDEEYWNSQKDILEEERAVPDRMCRHNYELGGPM

1i3rB1

0.49

0.47

13.77

2.91

HHsearch

KKVITAFNEG----LKGGGGSLVGGGSGGGGSRPWFLEYCKSECHFYNGTQRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNF

3lqzB1

0.86

0.71

19.91

1.83

FFAS-3D

---------------------LPFLPSTGGSSPENYLFQGRQECYAFNGTQRFLERYIYNREEFVRFDSDVGEFRAVTELGRPDEEYWNSQKDILEEERAVPDRMCRHNYELGGPM

4iiqC

0.10

3.79

0.97

EigenThreader

SQLEPRALWMEEHWERYTQLLRGWQQAFKVNHSGFHTYQRMIGCELLEGSITGFLQYAYDGQDFLIFNKDTLSWMAMDNVADIIRRVWEANRHELQYQKNWLEEECIAWLKRFLEY

1t7vA

0.12

0.11

3.94

1.68

CNFpred

----------QKAREDIFMETLKDIVEYYKDSTGSHVLQGRFGCEIENRSSGAFWKYYYDGKDYIEFNKEIPAWVPFDPAAQITKQKWEAEPVYVQRAKAYLEEECPATLRKYLKY

6kvmB

0.45

0.34

9.82

1.00

DEthreader

---------------------------RPSA--FF-FCGAISECHYLNERVRYLQRYIYNRQQYAHFDSDVGKFVADSPLGEPQAEYWNSNAELLENRMNEVDRFCRHNYGETVQR

(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	0.6703

(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	4s0uC	0.82	2.45	0.190	1.000	model1_4s0uC.pdb.gz
2	1kcgC	0.80	2.32	0.170	0.966	model1_1kcgC.pdb.gz
3	1a6zA	0.78	2.67	0.155	1.000	model1_1a6zA.pdb.gz
4	3dbxA1	0.77	2.61	0.060	0.991	model1_3dbxA1.pdb.gz
5	3jvgB	0.74	3.08	0.181	1.000	model1_3jvgB.pdb.gz
6	1je6A	0.73	2.91	0.122	0.991	model1_1je6A.pdb.gz
7	1frtA1	0.72	2.84	0.122	0.983	model1_1frtA1.pdb.gz
8	3ov6A	0.72	3.19	0.106	0.957	model1_3ov6A.pdb.gz
9	2h26A1	0.72	3.40	0.114	0.983	model1_2h26A1.pdb.gz
10	4f7cA	0.72	3.11	0.072	0.948	model1_4f7cA.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:0003823	0.79	antigen binding
GO:0042605	0.58	peptide antigen 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	0.88	biological regulation
GO:0050789	0.87	regulation of biological process
GO:0002376	0.82	immune system process
GO:0002682	0.79	regulation of immune system process
GO:0050794	0.72	regulation of cellular process
GO:0048518	0.64	positive regulation of biological process
GO:0002478	0.62	antigen processing and presentation of exogenous peptide antigen
GO:0048522	0.61	positive regulation of cellular process
GO:0019886	0.61	antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0050863	0.60	regulation of T cell activation
GO:0048583	0.60	regulation of response to stimulus
GO:0048584	0.58	positive regulation of response to stimulus
GO:0050896	0.56	response to stimulus
GO:0009987	0.55	cellular process
GO:0048519	0.53	negative regulation of biological 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:0044464	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.96	cytoplasmic part
GO:0044425	0.94	membrane part
GO:0016020	0.84	membrane
GO:0044459	0.80	plasma membrane part
GO:0044446	0.71	intracellular organelle part
GO:0098588	0.68	bounding membrane of organelle
GO:0098805	0.67	whole membrane
GO:0044437	0.67	vacuolar part
GO:0005765	0.66	lysosomal membrane
GO:0043226	0.61	organelle
GO:0043227	0.60	membrane-bounded organelle
GO:0016021	0.58	integral component of membrane
GO:0005886	0.58	plasma membrane
GO:0010008	0.57	endosome membrane
GO:0032991	0.56	macromolecular complex
GO:0031902	0.56	late endosome membrane
GO:0043234	0.55	protein complex
GO:0098797	0.54	plasma membrane protein complex
GO:0042613	0.53	MHC class II protein complex

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	2vxoB	0.488	3.65	0.071	0.767	6.3.5.2	NA
2	0.060	1t3cA	0.480	4.23	0.038	0.802	3.4.24.69	NA
3	0.060	2gajB	0.502	4.40	0.064	0.828	5.99.1.2	NA
4	0.060	1es0B	0.677	2.38	0.505	0.810	4.1.1.15	88
5	0.060	1rsrB	0.481	4.00	0.032	0.759	1.17.4.1	80

	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	0.10	3sdaA	0.713	3.26	0.096	0.974	0.58	GCY	complex1.pdb.gz	30,59,74,80,81,88,91,94
2	0.09	3ma7C	0.705	3.20	0.106	0.957	0.47	CD4	complex2.pdb.gz	25,26,39,43,54,56,73,80,81,92,99
3	0.07	3quyA	0.719	3.17	0.070	0.974	0.54	QUY	complex3.pdb.gz	27,40,42,59,74,81,88,91,93,94,97,98,105,108
4	0.07	3quxA	0.718	3.20	0.070	0.974	0.54	QUX	complex4.pdb.gz	30,40,57,59,74,88,91,93,94,98,106,109
5	0.03	1frt2	0.721	2.84	0.122	0.983	0.40	III	complex5.pdb.gz	56,57,58,59,74,75,76,85
6	0.01	1n368	0.306	4.23	0.030	0.491	0.45	III	complex6.pdb.gz	71,72,73,74,75

	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.