To Decipher the Mycoplasma hominis Proteins Targeting into the Endoplasmic Reticulum and Their Implications in Prostate Cancer Etiology Using Next-Generation Sequencing Data
Abstract
:1. Introduction
2. Results
2.1. Selection of the Whole Proteome Database of M. hominis
2.2. Prediction of the Subcellular Localization by cNLS Mapper
2.3. Prediction of ER Localization in M. hominis Proteins Using Hum-Mploc 3.0
3. Discussion
4. Materials and Methods
4.1. Proteins and Prediction Analysis
4.2. Choice of Protein Database for M. hominis
4.3. Prediction of the Subcellular Localization by cNLS Mapper
4.4. Prediction of ER Localization in M. hominis Proteins Using Hum-Mploc 3.0
5. Conclusions
Author Contributions
Acknowledgments
Conflicts of Interest
References
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Sample Availability: Not available. |
NLS | NLS Cutoff | Number of Proteins Targeting ER | Total Number of Proteins in This Range | Percentage |
---|---|---|---|---|
Monopartite NLS | 0–3.0 | 15 | 509 | 2.94 |
3.0–5.0 | 3 | 32 | 9.3 | |
5.0–8.0 | 1 | 16 | 6.25 | |
>8.0 | 0 | 6 | 0 | |
Bipartite NLS | 0–3.0 | 6 | 76 | 7.89 |
3.0–5.0 | 11 | 290 | 3.79 | |
5.0–8.0 | 2 | 194 | 1.03 | |
>8.0 | 0 | 3 | 0 |
Molecular Weight | Number of Proteins Targeting to ER | Total Number of Proteins | Percentage |
---|---|---|---|
0–20 kDa | 3 | 128 | 2.34 |
20–40 kDa | 10 | 205 | 4.87 |
40–60 kDa | 4 | 109 | 3.66 |
60–80 kDa | 1 | 61 | 1.63 |
>80 kDa | 1 | 60 | 1.66 |
Range of pI Value | Number of Proteins Targeting to ER | Total Number of Proteins | Percentage |
---|---|---|---|
3.0–5.0 | 0 | 25 | 0 |
5.0–6.0 | 1 | 105 | 0.95 |
6.0–7.0 | 0 | 68 | 0 |
7.0–8.0 | 0 | 35 | 0 |
8.0–9.0 | 2 | 109 | 1.83 |
9.0–10.0 | 12 | 181 | 6.62 |
10.0–11.0 | 4 | 33 | 12.12 |
12.0–13.0 | 0 | 7 | 0 |
Accession Number | Protein Name | Function in Bacteria | Protein Existence | pI | Molecular Weight | NLS Mapper | Hum-mPLoc 3.0 | |
---|---|---|---|---|---|---|---|---|
Monopartite | Bipartite | |||||||
A0A097NT54 | Uncharacterized protein | Unknown | Protein predicted | 10.17 | 13,450 | 0 | 22 | Endoplasmic reticulum |
A0A097NSU8 | Uncharacterized protein | Unknown | Protein predicted | 5.45 | 36,963 | 0 | 3.8 | Endoplasmic reticulum |
A0A097NTC6 | Lipoprotein signal peptidase (EC 3.4.23.36) | Aspartic-type endopeptidase activity. | Protein inferred from homology | 8.44 | 23,620 | 0 | 3.3 | Endoplasmic reticulum |
A0A097NTZ8 | Cation transporting P-type ATPase (EC 3.6.3.8) | ATP binding, calcium-transporting ATPase activity, and metal ion binding activity. | Protein inferred from homology | 8.56 | 107,148 | 2 | 6.1 | Endoplasmic reticulum |
A0A097NT87 | Protein translocase subunit SecY | Intracellular protein transmembrane transport activity, protein transport activity hrough the Sec complex | Protein inferred from homology | 9.51 | 54,926 | 6 | 3.9 | Endoplasmic reticulum |
A0A097NTV1 | Membrane protein | Unknown | Protein predicted | 9.54 | 25,294 | 0 | 5.5 | Endoplasmic reticulum |
A0A097NTF0 | Prolipoprotein diacylglyceryl transferase (EC 2.4.99.-) | Phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activity and involved in lipoprotein biosynthetic process. | Protein inferred from homology | 9.56 | 35,944 | 0 | 3.8 | Endoplasmic reticulum |
A0A097NSJ5 | Potassium transporter KtrB | Cation transmembrane transporter activity. | Protein predicted | 9.6 | 58,434 | 0 | 3 | Endoplasmic reticulum |
A0A097NT10 | ComEC/Rec2-related protein | Unknown | Protein predicted | 9.65 | 54,059 | 0 | 4.4 | Endoplasmic reticulum |
A0A097NSI4 | Uncharacterized protein | Unknown | Protein predicted | 9.66 | 38,283 | 0 | 3.3 | Endoplasmic reticulum |
A0A097NSM2 | Membrane protein | Unknown | Protein predicted | 9.72 | 33,519 | 0 | 3.4 | Endoplasmic reticulum |
A0A097NSJ8 | 1-acyl-sn-glycerol-3-phosphate acyltransferase (EC 2.3.1.51) | 1-acylglycerol-3-phosphate O-acyltransferase activity. | Protein predicted | 9.79 | 31,034 | 0 | 4.7 | Endoplasmic reticulum |
A0A097NT14 | Cobalt ABC transporter permease | Unknown | Protein predicted | 9.85 | 35,998 | 5 | 4.4 | Endoplasmic reticulum |
A0A097NTJ8 | ABC transporter permease | Transporter activity. | Protein inferred from homology | 9.86 | 65,590 | 0 | 2.9 | Endoplasmic reticulum |
A0A097NTE8 | Uncharacterized protein | Unknown | Protein predicted | 9.9 | 57,701 | 0 | 5 | Endoplasmic reticulum |
A0A097NSN9 | Uncharacterized protein | Unknown | Protein predicted | 9.97 | 14,493 | 0 | 2.6 | Endoplasmic reticulum |
A0A097NSG1 | Uncharacterized protein | Unknown | Protein predicted | 10.1 | 17,661 | 4 | 2.6 | Endoplasmic reticulum |
A0A097NTR2 | Membrane protein | Transporter activity. | Protein predicted | 10.19 | 33,456 | 4 | 3.2 | Endoplasmic reticulum |
A0A097NT45 | Membrane protein | Unknown | Protein predicted | 10.47 | 20,769 | 0 | 2.5 | Endoplasmic reticulum |
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Zakariah, M.; Khan, S.; Chaudhary, A.A.; Rolfo, C.; Ben Ismail, M.M.; Alotaibi, Y.A. To Decipher the Mycoplasma hominis Proteins Targeting into the Endoplasmic Reticulum and Their Implications in Prostate Cancer Etiology Using Next-Generation Sequencing Data. Molecules 2018, 23, 994. https://doi.org/10.3390/molecules23050994
Zakariah M, Khan S, Chaudhary AA, Rolfo C, Ben Ismail MM, Alotaibi YA. To Decipher the Mycoplasma hominis Proteins Targeting into the Endoplasmic Reticulum and Their Implications in Prostate Cancer Etiology Using Next-Generation Sequencing Data. Molecules. 2018; 23(5):994. https://doi.org/10.3390/molecules23050994
Chicago/Turabian StyleZakariah, Mohammed, Shahanavaj Khan, Anis Ahmad Chaudhary, Christian Rolfo, Mohamed Maher Ben Ismail, and Yousef Ajami Alotaibi. 2018. "To Decipher the Mycoplasma hominis Proteins Targeting into the Endoplasmic Reticulum and Their Implications in Prostate Cancer Etiology Using Next-Generation Sequencing Data" Molecules 23, no. 5: 994. https://doi.org/10.3390/molecules23050994