Table 1.
Proteins identified in the extraction of surface proteins non-covalently bound to the cell wall using guanidine hydrochloride of CB 129 wild-type and CB129ΔslpB strains1.
| Strain | Wild-type | CB129ΔslpB | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Group IDa | Sub-group IDb | locus_tag | Protein descriptionc | SurfG+d | COG lettere | MWf | log(e-value)g | Coverageh | Uniquesi | Specific uniquesj | emPAIk | log(e-value)g | Coverageh | Uniquesi | Specific uniquesj | emPAIk |
| a1 | a1.a1 | PFCIRM129_05460 | Surface protein with SLH domain (S-layer protein E) | SEC | O | 59.2 | −125.6 | 50 | 19 | 18 | 47.3 | −138.8 | 55 | 18 | 17 | 41.8 |
| a1 | a1.a2 | PFCIRM129_00700 | Surface layer protein B (S-layer protein B) | SEC | O | 56.8 | −263.2 | 74 | 34 | 33 | 37274.9 | – | – | – | – | – |
| a1 | a1.a3 | PFCIRM129_09350 | Surface layer protein A (S-layer protein A) | SEC | O | 58.3 | −174.3 | 75 | 24 | 23 | 16.0 | −143.5 | 68 | 22 | 21 | 9.0 |
| a2 | a2.a1 | PFCIRM129_12235 | Internaline A | SEC | S | 145.5 | −464.8 | 67 | 53 | – | 89.1 | −426.3 | 65 | 49 | – | 42.3 |
| a3 | a3.a1 | PFCIRM129_03680 & PFCIRM129_03685 | MERGED = TRUE | – | – | 95.9 | −186.7 | 43 | 18 | – | 283.8 | −196.6 | 47 | 20 | – | 431.9 |
| a4 | a4.a1 | PFCIRM129_10100 | 60 kDa chaperonin 2 (Protein Cpn60 2) (groEL protein 2) (Heat shock protein 60 2) | CYT | O | 56.4 | −82.5 | 38 | 13 | – | 5.3 | −112.6 | 49 | 18 | – | 14.8 |
| a5 | a5.a1 | PFCIRM129_07835 | 60 kDa chaperonin 1 (Protein Cpn60 1) (groEL protein 1) (Heat shock protein 60 1) | CYT | O | 56 | −89.2 | 38 | 12 | – | 2.2 | −134.7 | 60 | 21 | – | 7.5 |
| a6 | a6.a1 | PFCIRM129_06355 | Chaperone clpB 2 (ATP-dependent Clp protease B2) (Clp chaperone) | CYT | O | 94.2 | −39.6 | 19 | 10 | 9 | 1.2 | −103.0 | 29 | 18 | – | 3.0 |
| a7 | a7.a1 | PFCIRM129_06315 | Chaperone protein dnaK 1 (Heat shock protein 70 1) (Heat shock 70 kDa protein 1) (HSP70 1) | CYT | O | 65.3 | −24.0 | 13 | 5 | 0.6 | −61.2 | 34 | 15 | 12 | 3.8 | |
| a7 | a7.a2 | PFCIRM129_08775 | Chaperone protein dnaK 2 (Heat shock protein 70 2) (Heat shock 70 kDa protein 2) (HSP70 2) | CYT | O | 67.1 | – | – | – | – | – | −43.7 | 23 | 10 | 7 | 2.0 |
| a9 | a9.a1 | PFCIRM129_08275 | Elongation factor Tu | CYT | J | 43.6 | −43.7 | 33 | 7 | – | 2.0 | −32.4 | 28 | 7 | – | 3.4 |
| b11 | b11.a1 | PFCIRM129_11405 | 30S ribosomal protein S1 | CYT | J | 53.5 | −5.4 | 7 | 2 | – | 0.3 | −58.9 | 27 | 8 | – | 1.6 |
| b12 | b12.a1 | PFREUD_01840 | Pyruvate synthase/Pyruvate-flavodoxin oxidoreductase | CYT | C | 136.4 | – | – | – | – | – | −67.5 | 16 | 14 | – | 1.2 |
| b13 | b13.a1 | PFCIRM129_10305 | Methylmalonyl-CoA carboxytransferase 5S subunit. (transcarboxylase 5S) 505 bp | CYT | C | 55.5 | −23.3 | 16 | 5 | – | 0.7 | −37.1 | 23 | 9 | – | 1.8 |
| b14 | b14.a1 | PFCIRM129_06950 | Trigger factor (TF) | CYT | O | 57.3 | −8.3 | 6 | 2 | – | 0.3 | −36.7 | 20 | 6 | – | 2.0 |
| b15 | b15.a1 | PFCIRM129_07240 | Methylmalonyl-CoA mutase large subunit (Methylmalonyl-CoA mutase alpha subunit) (MCM-alpha) (MUTB-(R)-2-Methyl-3-oxopropanoyl-CoA CoA-carbonylmutase) | CYT | I | 80.1 | −15.6 | 7 | 4 | – | 0.4 | −38.3 | 15 | 8 | – | 1.0 |
| b16 | b16.a1 | PFCIRM129_06070 | Enolase 1 | CYT | G | 45.9 | −26.5 | 20 | 5 | – | 1.1 | −41.5 | 25 | 7 | – | 1.7 |
| b17 | b17.a1 | PFCIRM129_07235 | Methylmalonyl-CoA mutase small subunit (Methylmalonyl-CoA mutase beta subunit) (MCB-beta) | CYT | I | 69.5 | −16.2 | 9 | 4 | – | 0.4 | −59.4 | 26 | 9 | – | 1.2 |
| b19 | b19.a1 | PFCIRM129_10180 | Iron-sulfur protein | CYT | C | 57.2 | −26.1 | 18 | 6 | – | 1.1 | −16.7 | 8 | 3 | – | 0.4 |
| b20 | b20.a1 | PFCIRM129_08670 | Cell-wall peptidases, NlpC/P60 family SEC protein | SEC | M | 58.7 | −51.6 | 22 | 8 | – | 1.7 | −9.5 | 6 | 2 | – | 0.4 |
| b21 | b21.a1 | PFCIRM129_09300 | FAD-dependent pyridine nucleotide-disulphide oxidoreductase:4Fe-4S ferredoxin, iron-sulfur binding:Aromatic-ring hydroxylase | CYT | C | 59.7 | – | – | – | – | – | −42.1 | 20 | 8 | – | 1.2 |
| b22 | b22.a1 | PFCIRM129_00205 | Succinate dehydrogenase flavoprotein subunit | CYT | C | 74.7 | −17.1 | 5 | 3 | – | 0.3 | −20.8 | 6 | 4 | – | 0.5 |
| b23 | b23.a1 | PFCIRM129_08495 | NADH-quinone oxidoreductase chain G (NADH dehydrogenase I, chain G) | CYT | C | 84.8 | −22.3 | 6 | 3 | – | 0.2 | −28.3 | 9 | 5 | – | 0.4 |
| b24 | b24.a1 | PFCIRM129_09980 | Peptidyl-prolyl cis-trans isomerase | SEC | O | 35.9 | −23.0 | 22 | 4 | – | 5.8 | −11.5 | 7 | 2 | – | 1.2 |
| b25 | b25.a1 | PFCIRM129_10295 | Methylmalonyl-CoA carboxytransferase 12S subunit (EC2.1.3.1) (Transcarboxylase 12S subunit). 610 bp | CYT | I | 56.3 | −31.2 | 11 | 5 | – | 0.7 | −15.2 | 7 | 3 | – | 0.4 |
| b26 | b26.a1 | PFCIRM129_11300 | Glyceraldehyde-3-phosphate dehydrogenase / erythrose 4 phosphate dehydrogenase | CYT | G | 37.7 | −48.7 | 39 | 9 | – | 2.9 | – | – | – | – | – |
| b27 | b27.a1 | PFCIRM129_05155 | ATP synthase subunit alpha (ATPase subunit alpha) (ATP synthase F1 sector subunit alpha) | CYT | C | 58.8 | −7.9 | 5 | 2 | – | 0.2 | −17.9 | 11 | 5 | – | 0.6 |
| b30 | b30.a1 | PFREUD_10490 | ATP synthase subunit beta (ATPase subunit beta) (ATP synthase F1 sector subunit beta) | CYT | C | 52.4 | −12.0 | 9 | 3 | – | 0.4 | −15.0 | 12 | 4 | – | 0.7 |
| b31 | b31.a1 | PFCIRM129_11080 & PFCIRM129_11085 | MERGED = TRUE | – | – | 35.4 | – | – | – | – | – | −17.1 | 20 | 4 | – | 0.9 |
| b32 | b32.a1 | PFCIRM129_10995 | Glycerol kinase (ATP:glycerol 3-phosphotransferase) (Glycerokinase) (GK) | CYT | C | 55.6 | – | – | – | – | – | −17.7 | 11 | 5 | – | 1.3 |
| b33 | b33.a1 | PFCIRM129_01440 | Coenzyme A transferase (Putative succinyl-CoA or butyryl-CoA:coenzyme A transferase) | CYT | C | 55.6 | – | – | – | – | – | −14.5 | 7 | 3 | – | 0.5 |
| b34 | b34.a1 | PFCIRM129_11710 & PFCIRM129_11715 | MERGED = TRUE | – | – | 58.8 | −12.1 | 4 | 2 | – | 0.4 | −30.6 | 13 | 5 | – | 1.2 |
| b35 | b35.a1 | PFCIRM129_05730 | D-lactate dehydrogenase | CYT | C | 63.6 | −9.5 | 9 | 3 | – | 0.3 | −14.4 | 11 | 4 | – | 0.4 |
| b36 | b36.a1 | PFCIRM129_00390 | Cysteine synthase 2 | CYT | E | 33.5 | −40.2 | 38 | 6 | – | 1.7 | – | – | – | – | – |
| b37 | b37.a1 | PFCIRM129_08120 | Solute binding protein of the ABC transport system | SEC | E | 61.4 | −7.3 | 7 | 3 | – | 0.4 | −11.9 | 4 | 2 | – | 0.3 |
| b38 | b38.a1 | PFCIRM129_05105 | Hypothetical protein | CYT | – | 64 | – | – | – | – | – | −17.0 | 10 | 5 | – | 0.6 |
| b40 | b40.a1 | PFCIRM129_01500 | Pyruvate phosphate dikinase | CYT | G | 95.7 | – | – | —- | – | – | −11.2 | 3 | 2 | – | 0.1 |
| b41 | b41.a1 | PFCIRM129_03550 | Alanine dehydrogenase | CYT | E | 39.3 | – | – | – | – | – | −5.8 | 6 | 2 | – | 0.4 |
| b43 | b43.a1 | PFCIRM129_10420 | iolA (Myo-inositol catabolism IolA protein) (Methylmalonic acid semialdehyde dehydrogenase) | CYT | C | 52.7 | – | – | – | – | – | −9.1 | 6 | 2 | – | 0.3 |
| b44 | b44.a1 | PFCIRM129_08025 | Resuscitation-promoting factor | SEC | L | 37.7 | −15.9 | 11 | 2 | – | 0.9 | – | – | – | – | – |
| b45 | b45.a1 | PFREUD_14570 | Polyribonucleotide nucleotidyltransferase (Polynucleotide phosphorylase) (PNPase) (Guanosine pentaphosphate synthetase) | CYT | J | 79.3 | – | – | – | – | – | −9.5 | 3 | 2 | – | 0.2 |
| b46 | b46.a1 | PFCIRM129_08280 | Elongation factor G (EF-G) | CYT | J | 76.5 | – | – | – | – | – | −5.4 | 2 | 2 | – | 0.2 |
| b48 | b48.a1 | PFCIRM129_08935 | FAD linked oxidase domain protein | CYT | C | 100.4 | – | – | – | – | – | −18.2 | 5 | 3 | – | 0.2 |
| b49 | b49.a1 | PFCIRM129_08300 | DNA-directed RNA polymerase beta chain (RNAP beta subunit) (Transcriptase beta chain) (RNA polymerase subunit beta) | CYT | K | 128.5 | – | – | – | – | – | −8.8 | 3 | 2 | – | 0.1 |
| b50 | b50.a1 | PFCIRM129_00200 | Succinate dehydrogenase | CYT | C | 27 | −8.4 | 10 | 2 | – | 0.6 | – | – | – | – | – |
| b51 | b51.a1 | PFCIRM129_10175 | Hypothetical protein | CYT | S | 23.1 | −11.5 | 16 | 2 | – | 0.7 | – | – | – | – | – |
The Group to which the protein belongs. All the proteins in a group have at least one peptide in common.
The Sub-Group to which the protein belongs. All the proteins in a sub-group are identified with the same valid peptides.
Protein description as it appears in the header of the fasta file.
SurfG+ localization prediction.
Cluster of Orthologous Group category – A, RNA processing and modification; B, Chromatin Structure and dynamics; C, Energy production and conversion; D, Cell cycle control and mitosis; E, Amino Acid metabolis and transport; F, Nucleotide metabolism and transport; G, Carbohydrate metabolism and transport; H, Coenzyme metabolis; I, Lipid metabolism; J, Translation; K, Transcription; L, Replication and repair; M, Cell wall/membrane/envelope biogenesis; N, Cell motility; O, Post-translational modification; P, Inorganic ion transport and metabolism; Q, Secondary Structure; T, Signal Transduction; U, Intracellular trafficking and secretion; Y, Nuclear structure; Z, Cytoskeleton; R, General Functional Prediction only; S, Function Unknown.
Molecular weight of the protein expressed in KDa.
Protein e-value expressed in log. Statistical value representing the number of times this protein would be identified randomly. Calculated as the product of unique peptide e-values in the sample.
Percentage of protein sequence covered by identified peptides.
The number of unique peptide sequence assigned to this protein.
The number of unique peptide sequence specific to this subgroup of proteins. It is only available if there are more than one subgroup within a group.
The Exponentially Modified Protein Abundance Index (emPAI) computation (Ishihama et al., 2005).
Part of these results were previously published in do Carmo et al. (2017).