TABLE 2.
Phage PR1 structural proteins identified by nanoLC-ESI-MS/MSa
| Protein | Identified function | Band no. (most abundant)b | Protein mass (Da) | No. of unique peptidesc | Sequence coverage (%) | HHpred significant match (phage) | E-valued | Identity (%)e |
|---|---|---|---|---|---|---|---|---|
| gp4 | DNA transfer protein | 1–7 (4) | 65,166 | 12 | 23.7 | DNA transfer protein (enterobacterial phage DT57C) | 2e−164 | 47 |
| gp8 | Hypothetical protein | 1–11 (1) | 40,622 | 8 | 39.0 | Hypothetical protein My1_019 (Pectobacterium phage My1) | 7e−19 | 39 |
| gp18 | No hit | 2, 7 | 34,021 | 3 | 11.6 | |||
| gp46 | Holin | 11 | 25,959 | 4 | 22.6 | Putative holin (Pectobacterium phage My1) | 3e−69 | 48 |
| gp48 | Deoxynucleoside monophosphate kinase | 11 | 26,205 | 3 | 16.7 | Deoxynucleoside-5′-monophosphate kinase (Escherichia phage Akfv33) | 1e−24 | 36 |
| gp82 | Hypothetical protein | 14 | 22,008 | 5 | 20.7 | Hypothetical protein Ea357_046 (Erwinia phage Ea35-70) | 9e−63 | 55 |
| gp101 | Ribonucleoside-diphosphate reductase | 1 | 92,766 | 3 | 5.2 | Aerobic ribonucleoside diphosphate reductase, large subunit (Escherichia phage vb_ecos_FFH1) | 0.0 | 58 |
| gp102 | Starvation-inducible protein | 1 | 29,514 | 2 | 8.8 | Phosphate starvation-inducible protein PhoH, predicted ATPase (Yersinia phage ϕR201) | 2e−101 | 60 |
| gp121 | DNA polymerase | 1 | 69,415 | 2 | 4.1 | DNA polymerase (Escherichia phage vB_EcoS_FFH1) | 0.0 | 68 |
| gp128 | Hypothetical protein | 7 | 31,602 | 6 | 29.9 | D11 protein (enterobacterial phage DT57C) | 2e−39 | 36 |
| gp134 | Hypothetical protein | 1–10 (4) | 81,973 | 24 | 41.5 | Hypothetical protein OO7_12349 (Providencia sneebia DSM 19967) | 1e−71 | 47 |
| gp135 | Tail protein | 6 | 15,421 | 1 | 7.1 | Tail protein (Salmonella phage Stitch) | 2e−27 | 42 |
| gp136 | Tail protein | 1–9 (1, 2) | 110,749 | 27 | 38.6 | Tail protein Pb4 (Salmonella phage Spc35) | 1e−173 | 45 |
| gp137 | Baseplate hub protein | 1–9 (2) | 106,764 | 23 | 31.0 | Tail protein Pb3 (Escherichia phage Akfv33) | 0.0 | 57 |
| gp138 | Distal tail protein | 12, 14 | 22,870 | 5 | 40 | Hypothetical protein SPC35_0127 (Salmonella phage Spc35) | 1e−72 | 57 |
| gp139 | Tape measure protein | 1–7 (2) | 134,015 | 46 | 48.6 | Tape measure protein (Salmonella phage Stitch) | 0.0 | 36 |
| gp142 | Minor tail protein | 9–11 (10) | 33,805 | 7 | 34.0 | Minor tail protein (Escherichia phage Akfv33) | 6e−56 | 42 |
| gp143 | Major tail protein | 1–11 (6) | 41,715 | 10 | 41.2 | Major tail protein (Salmonella phage Stitch) | 9e−165 | 60 |
| gp144 | Tail tube terminator protein | 14 | 20,192 | 2 | 8.0 | Tail terminator protein (enterobacterial phage DT57C) | 2e−36 | 41 |
| gp145 | Hypothetical protein | 10 | 28,397 | 5 | 22.7 | Hypothetical protein AGC_0158 (Escherichia phage Eps7) | 3e−88 | 55 |
| gp146 | Hypothetical protein | 13–14 (14) | 19,794 | 7 | 53.5 | Hypothetical protein BN79_156 (Yersinia phage ϕR201) | 9e−17 | 30 |
| gp147 | Major capsid protein | 1–14 (9) | 52,374 | 21 | 52.6 | Phage capsid family protein (Escherichia phage slur09) | 8e−153 | 56 |
| gp148 | Prohead protease | 1–14 (13) | 22,091 | 6 | 40.6 | Putative prohead protease (Escherichia phage vb_ecos_FFH1) | 8e−74 | 62 |
| gp149 | No hit | 1–14 (5) | 44,254 | 26 | 70.2 | |||
| gp150 | Portal protein | 1–7 (6, 7) | 46,128 | 16 | 51.1 | Portal protein (Yersinia phage ϕR201) | 0.0 | 63 |
| gp154 | No hit | 1–5 (4) | 68,027 | 9 | 18.7 |
a
It should be noted that identifications with a low abundance of peptides (<4) could be the result of protein impurities remaining in the samples.
b
SDS-PAGE band.
c
Only phage proteins with a minimum number of two unique peptides were considered (except gp135 based on a reliable function).
d
HHpred E-value of the most significant matching protein model.
e
HHpred percent sequence identity for a pairwise amino acid alignment with the template protein.