D-I-TASSER P07998-D1

D-I-TASSER results for P07998-D1

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

Input Sequence in FASTA format

>P07998 (156 residues)
MALEKSLVRLLLLVLILLVLGWVQPSLGKESRAKKFQRQHMDSDSSPSSSSTYCNQMMRR
RNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRY
PNCAYRTSPKERHIIVACEGSPYVPVHFDASVEDST

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MALEKSLVRLLLLVLILLVLGWVQPSLGKESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVEDST
Prediction	CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCSSSSCCCHHHHHHHHCCCCCCCCCCCCCSSSCCCCSSSSSSSSCCCCCCCCCCCCCCCCSCSSSSSSCCCCCSCSSSCCSSCCCC
Confidence	985502579999999999987226777888589999997328999999881477999997467789888833665599899988756898348789986265599267689983699889998633112110599982699732267411514889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MALEKSLVRLLLLVLILLVLGWVQPSLGKESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVEDST
Prediction	764444233233332312220112332356341540342023374457444520140044242457413531001014273034005457241644452134156404013031365663450516445543100000374430000014315668
	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

CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCSSSSCCCHHHHHHHHCCCCCCCCCCCCCSSSCCCCSSSSSSSSCCCCCCCCCCCCCCCCSCSSSSSSCCCCCSCSSSCCSSCCCC
MALEKSLVRLLLLVLILLVLGWVQPSLGKESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVEDST

3mwqA1

0.64

0.52

14.83

1.17

DEthreader

----------------------------KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVC-SQKNVACKNGQNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASVSGRS

1rraA

0.65

0.52

14.81

4.72

SPARKS-K

----------------------------AESSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNGRNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV----

3mwqA1

0.69

0.55

15.69

1.21

MapAlign

-----------------------------ETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASVSG--

3mwqA1

0.68

0.56

15.88

1.07

CEthreader

----------------------------KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASVSGRS

1rraA

0.65

0.52

14.81

3.20

MUSTER

----------------------------AESSADKFKRQHMDTEGPSKSSPTYCNQMMKRQGMTKGSCKPVNTFVHEPLEDVQAICSQGQVTCKNGRNNCHKSSSTLRITDCRLKGSSKYPNCDYTTTDSQKHIIIACDGNPYVPVHFDASV----

3mwqA

0.59

0.57

16.37

2.96

HHsearch

NCAYKTTQANKHIIVACEGNGRSGRSGK-ETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV----

3mwqA1

0.68

0.56

15.88

1.98

FFAS-3D

----------------------------KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASVSGRS

3mwqA1

0.68

0.56

15.88

1.22

EigenThreader

----------------------------KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASVSGRS

2e0jA

0.98

0.81

22.63

2.82

CNFpred

----------------------------KESRAKKFQRQHMDSDSSPSSSSTYCNQMMLLRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVEDST

3mwqA

0.64

0.52

14.83

1.17

DEthreader

----------------------------KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVC-SQKNVACKNGQNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASVSGRS

(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	0.7147

(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	3mwqA	0.84	2.20	0.592	0.917	model1_3mwqA.pdb.gz
2	1rraA	0.77	0.98	0.653	0.795	model1_1rraA.pdb.gz
3	2rnfA	0.72	1.32	0.433	0.763	model1_2rnfA.pdb.gz
4	4x09A	0.69	1.72	0.361	0.750	model1_4x09A.pdb.gz
5	2zpoA	0.69	1.89	0.414	0.744	model1_2zpoA.pdb.gz
6	1qmtA	0.68	1.87	0.333	0.750	model1_1qmtA.pdb.gz
7	1k2aA	0.68	1.98	0.339	0.750	model1_1k2aA.pdb.gz
8	1k59A	0.68	1.84	0.353	0.744	model1_1k59A.pdb.gz
9	2j4tA	0.68	1.82	0.379	0.744	model1_2j4tA.pdb.gz
10	2vq9A	0.68	1.83	0.328	0.744	model1_2vq9A.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:0004540	1.00	ribonuclease activity
GO:0004519	0.89	endonuclease 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:0009987	0.96	cellular process
GO:0071704	0.94	organic substance metabolic process
GO:1901360	0.93	organic cyclic compound metabolic process
GO:0044699	0.93	single-organism process
GO:0044238	0.93	primary metabolic process
GO:0034641	0.93	cellular nitrogen compound metabolic process
GO:0016070	0.92	RNA metabolic process
GO:0065007	0.88	biological regulation
GO:0050896	0.85	response to stimulus
GO:0050794	0.83	regulation of cellular process
GO:0006950	0.83	response to stress
GO:0048522	0.81	positive regulation of cellular process
GO:0044767	0.80	single-organism developmental process
GO:0044763	0.80	single-organism cellular process
GO:0032879	0.78	regulation of localization
GO:0090501	0.77	RNA phosphodiester bond hydrolysis
GO:0090502	0.76	RNA phosphodiester bond hydrolysis, endonucleolytic
GO:0048646	0.76	anatomical structure formation involved in morphogenesis
GO:0044710	0.74	single-organism metabolic process
GO:0050790	0.72	regulation of catalytic activity
GO:0016043	0.72	cellular component organization
GO:1901576	0.71	organic substance biosynthetic process
GO:0048523	0.71	negative regulation of cellular process
GO:0044271	0.71	cellular nitrogen compound biosynthetic process
GO:0008284	0.71	positive regulation of cell proliferation
GO:0051223	0.70	regulation of protein transport
GO:0051050	0.70	positive regulation of transport
GO:0044711	0.70	single-organism biosynthetic process
GO:0006629	0.70	lipid metabolic process
GO:0006351	0.70	transcription, DNA-templated
GO:1903532	0.69	positive regulation of secretion by cell
GO:0098781	0.69	ncRNA transcription
GO:0051258	0.69	protein polymerization
GO:0050708	0.69	regulation of protein secretion
GO:0050679	0.69	positive regulation of epithelial cell proliferation
GO:0048660	0.69	regulation of smooth muscle cell proliferation
GO:0046463	0.69	acylglycerol biosynthetic process
GO:0046339	0.69	diacylglycerol metabolic process
GO:0036293	0.69	response to decreased oxygen levels
GO:0032430	0.69	positive regulation of phospholipase A2 activity
GO:0010863	0.69	positive regulation of phospholipase C activity
GO:0008285	0.69	negative regulation of cell proliferation
GO:0008154	0.69	actin polymerization or depolymerization
GO:0001936	0.69	regulation of endothelial cell proliferation
GO:0051222	0.65	positive regulation of protein transport
GO:0001525	0.61	angiogenesis
GO:0009605	0.54	response to external stimulus
GO:0006952	0.54	defense response
GO:0051704	0.53	multi-organism process
GO:0042742	0.52	defense response to bacterium
GO:0050714	0.50	positive regulation of protein secretion
GO:0048856	0.50	anatomical structure development
GO:0048662	0.50	negative regulation of smooth muscle cell proliferation
GO:0032431	0.50	activation of phospholipase A2 activity
GO:0030041	0.50	actin filament polymerization
GO:0009303	0.50	rRNA transcription
GO:0007202	0.50	activation of phospholipase C activity
GO:0006651	0.50	diacylglycerol biosynthetic process
GO:0001938	0.50	positive regulation of endothelial cell proliferation
GO:0001666	0.50	response to hypoxia

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:0043227	0.93	membrane-bounded organelle
GO:0044421	0.86	extracellular region part
GO:0044464	0.81	cell part
GO:0044424	0.78	intracellular part
GO:0043229	0.63	intracellular organelle
GO:0043231	0.62	intracellular membrane-bounded organelle
GO:0044446	0.57	intracellular organelle part
GO:0005634	0.55	nucleus
GO:0043234	0.53	protein complex
GO:0032311	0.52	angiogenin-PRI complex
GO:0005615	0.51	extracellular space

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	0.179	1rnfA	0.724	1.31	0.433	0.763	3.1.27.-	NA
2	0.178	2rnfA	0.724	1.32	0.433	0.763	4.2.1.81	NA
3	0.176	1rraA	0.767	0.98	0.653	0.795	3.1.27.5	NA
4	0.173	2e0jA	0.781	1.24	0.984	0.821	3.1.27.5	NA
5	0.148	1agiA	0.696	2.06	0.331	0.776	3.1.27.-	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	0.57	3srnA	0.711	0.72	0.673	0.724	1.68	III	complex1.pdb.gz	32,33,36,40,73,75,83,86,93,94,99,100,101,102,109,132,133,134,135,136,137,138,139,140
2	0.37	1dfj0	0.779	0.66	0.702	0.795	1.78	III	complex2.pdb.gz	35,39,52,59,60,63,66,67,69,70,71,94,95,99,114,116,117,119,137,139,147
3	0.37	9rsa0	0.785	0.54	0.702	0.795	1.74	III	complex3.pdb.gz	70,89,90,91,92,93,94,111,113,114,116,126,128,132,135,149,152
4	0.36	1jn4A	0.780	0.66	0.702	0.795	1.49	139	complex4.pdb.gz	39,40,71,72,73,93,95,97,99,137,139,146,147,148

	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.