TABLE 2.
Strain-specific genes predicted in the TIRs of S. ambofaciens strains DSM40697 and ATCC23877
| Strain | Specific region | Gene | Producta | Identity (%)b | Overlap (%)c | Gene name | Plasmid | Organism |
|---|---|---|---|---|---|---|---|---|
| DSM40697 | A | DSMT0001 | Unknown | |||||
| DSMT0002 | Putative transcriptional regulator | |||||||
| DSMT0003 | Putative phage integrase | 35 | 93 | NocaDRAFT_4522 | Nocardioides sp. strain JS614 | |||
| DSMT0004 | Unknown | |||||||
| DSMT0005 | Putative serine/threonine protein kinase | |||||||
| DSMT0006 | Unknown | |||||||
| DSMT0007 | Unknown | |||||||
| DSMT0008 | Putative helicase | 83 | 88 | SAV7571 | Streptomyces avermitilis | |||
| DSMT0009 | Putative ATP-dependent DNA ligase | 64 | 98 | SAP1_90 (lig) | SAP1 | Streptomyces avermitilis | ||
| DSMT0010 | Putative integral membrane transport protein | 72 | 100 | SCO6809 | Streptomyces coelicolor | |||
| DSMT0011 | Putative secreted protein | 75 | 100 | SCO6811 | Streptomyces coelicolor | |||
| DSMT0012 | Putative FAD-dependent oxidoreductase | 58 | 98 | pREL1_0108 | pREL1 | Rhodococcus erythropolis | ||
| DSMT0013 | Putative transcriptional regulator | 95 | 96 | pFQ25.11 | Streptomyces sp. strain F2 | |||
| DSMT0014 | Putative phosphinothricin N-acetyltransferase | 77 | 99 | pFQ25.10 | Streptomyces sp. strain F2 | |||
| DSMT0015 | Unknown | |||||||
| DSMT0016 | Conserved hypothetical protein | 85 | 99 | pnf1840 | pNF1 | Nocardia farcinica | ||
| DSMT0017 | Putative membrane protein | 76 | 100 | SCO3280 | Streptomyces coelicolor | |||
| DSMT0018 | Putative glycosyl hydrolase, BNR repeat | 36 | 98 | ArthDRAFT_2101 | Arthrobacter sp. strain FB24 | |||
| DSMT0019 | Putative lipoprotein | 72 | 100 | SCO4458 | Streptomyces coelicolor | |||
| DSMT0020 | Putative membrane protein | 60 | 96 | SCO4459 | Streptomyces coelicolor | |||
| DSMT0021 | Putative monooxygenase | 78 | 94 | SCO6838 | Streptomyces coelicolor | |||
| DSMT0022 | Putative arsenic resistance membrane transport protein | 84 | 99 | SCO6837 | Streptomyces coelicolor | |||
| DSMT0023 | Putative transcriptional regulator | 82 | 100 | SCO3699 | Streptomyces coelicolor | |||
| DSMT0024 | Putative arsenate reductase | 87 | 95 | SCO6835 | Streptomyces coelicolor | |||
| DSMT0025 | Putative thioredoxin reductase | 79 | 99 | SCO6834 | Streptomyces coelicolor | |||
| DSMT0026 | Conserved hypothetical protein | 25 | 75 | Tfu_2935 | Thermobifida fusca | |||
| DSMT0027 | Unknown | |||||||
| DSMT0028 | Conserved hypothetical protein | 87 | 100 | SCP1.257 | SCP1 | Streptomyces coelicolor | ||
| DSMT0029 | Conserved hypothetical protein | 36 | 83 | SAP1_88 | SAP1 | Streptomyces avermitilis | ||
| DSMT0030 | Putative RNA polymerase sigma factor | 37 | 97 | SAP1_87 (sig) | SAP1 | Streptomyces avermitilis | ||
| DSMT0031 | Conserved hypothetical protein | 35 | 93 | SAP1_86 | SAP1 | Streptomyces avermitilis | ||
| DSMT0032 | Putative secreted protein | 84 | 100 | SCP1.323c | SCP1 | Streptomyces coelicolor | ||
| DSMT0033 | Putative secreted protein | 89 | 100 | SCP1.261c | SCP1 | Streptomyces coelicolor | ||
| DSMT0034 | Conserved hypothetical protein | 84 | 94 | SCP1.262 | SCP1 | Streptomyces coelicolor | ||
| DSMT0035 | Ttra helicase fragment (pseudogene) | 80 | 95 | SAV7571 | Streptomyces avermitilis | |||
| DSMT0036 | Conserved hypothetical protein DUF1099 | 63 | 95 | ShewDRAFT_1466 | Shewanella sp. strain PV-4 | |||
| DSMT0037 | Unknown | |||||||
| DSMT0038 | Conserved hypothetical protein (pseudogene) | 70 | 99 | SCO0085 | Streptomyces coelicolor | |||
| DSMT0039 | Putative ATP-dependent DNA ligase | 59 | 100 | SAP1_90 (lig) | SAP1 | Streptomyces avermitilis | ||
| DSMT0040 | Conserved hypothetical protein | 71 | 100 | SCO0048 | Streptomyces coelicolor | |||
| DSMT0041 | Unknown | |||||||
| DSMT0042 | Conserved hypothetical protein | 29 | 95 | SCP1.202 | SCP1 | Streptomyces coelicolor | ||
| DSMT0043 | Conserved hypothetical protein | 84 | 100 | SCP1.201 | SCP1 | Streptomyces coelicolor | ||
| DSMT0044 | Putative secreted protein | 94 | 100 | SCP1.200c | SCP1 | Streptomyces coelicolor | ||
| DSMT0045 | Putative secreted esterase | 93 | 100 | SCP1.199c | SCP1 | Streptomyces coelicolor | ||
| DSMT0046 | Putative transposase | 55 | 71 | Francci3_3385 | Frankia sp. strain CcI3 | |||
| DSMT0047 | Putative transporter | 55 | 93 | nfa29650 | Nocardia farcinica | |||
| DSMT0048 | Tpg protein fragment (pseudogene) | 75 | 97 | tpgSLP2 | SLP2 | Streptomyces lividans | ||
| DSMT0049 | Putative AraC-family transcriptional regulator (pseudogene) | 82 | 97 | SCO3804 | Streptomyces coelicolor | |||
| DSMT0050 | Conserved hypothetical protein | 73 | 48 | SCO3803 | Streptomyces coelicolor | |||
| DSMT0051 | Putative nourseothricin acetyltransferase | 69 | 100 | nat1 | Streptomyces noursei | |||
| DSMT0052 | Conserved hypothetical protein | 30 | 93 | Francci3_1866 | Frankia sp. strain CcI3 | |||
| DSMT0053 | Conserved hypothetical protein | 47 | 76 | Francci3_1863 | Frankia sp. strain CcI3 | |||
| DSMT0054 | Unknown | |||||||
| DSMT0055 | Putative peptidase | 38 | 98 | SCO3610 | Streptomyces coelicolor | |||
| DSMT0056 | Putative major facilitator superfamily | 29 | 93 | NocaDRAFT_1725 | Nocardioides sp. strain JS614 | |||
| B | DSMT0083 | Putative 3-oxoacyl-ACP synthase III | 40 | 100 | ArthDRAFT_2448 | Arthrobacter sp. strain FB24 | ||
| C | DSMT0085 | Putative ABC transport system ATP-binding protein | 64 | 93 | SCO0121 | Streptomyces coelicolor | ||
| DSMT0086 | Putative integral membrane protein | 44 | 93 | SCO0120 | Streptomyces coelicolor | |||
| DSMT0087 | Conserved hypothetical protein | 46 | 76 | Tfu_1509 | Thermobifida fusca | |||
| DSMT0088 | Conserved hypothetical protein | 31 | 98 | SCO0123 | Streptomyces coelicolor | |||
| DSMT0089 | Putative polyprenyl synthetase | 61 | 98 | SCO0568 | Streptomyces coelicolor | |||
| DSMT0090 | Putative geranylgeranyl diphosphate synthase | 48 | 100 | ggdps | Streptomyces sp. strain KO-3988 | |||
| D | DSMT0118 | Conserved hypothetical protein | 84 | 79 | SCP1.218c | SCP1 | Streptomyces coelicolor | |
| E | DSMT0134 | Unknown | ||||||
| ATCC23877 | a | SAMT0001 | Conserved hypothetical protein | 62 | 92 | SAV7573 | Streptomyces avermitilis | |
| SAMT0002 | Putative helicase | 84 | 100 | ttrA | SLP2 | Streptomyces lividans | ||
| SAMT0003 | Unknown | |||||||
| SAMT0004 | Conserved hypothetical protein | 42 | 100 | pFRL1.57 | pFRL1 | Streptomyces sp. strain FR1 | ||
| SAMT0005 | Unknown | 64 | 59 | pFRL1.57 | pFRL1 | Streptomyces sp. strain FR1 | ||
| SAMT0006 | Putative NTP pyrophosphohydrolase | 39 | 67 | PFL_4894 | Pseudomonas fluorescens | |||
| SAMT0007 | Conserved hypothetical protein | 52 | 95 | nfa38470 | Nocardia farcinica | |||
| SAMT0008 | Putative glyoxalase | 64 | 96 | nfa38460 | Nocardia farcinica | |||
| SAMT0009 | Putative ferredoxin NADPH reductase | 55 | 97 | nfa38450 | Nocardia farcinica | |||
| SAMT0010 | KilB-like protein, role in intramycelial spread | 48 | 95 | pRL2.23 | pRL2 | Streptomyces sp. strain 44414 | ||
| SAMT0011 | Putative acetyltransferase | 50 | 100 | SAV2967 | Streptomyces avermitilis | |||
| b | SAMT0023 | Unknown | ||||||
| SAMT0024 | Putative hydrolase | 53 | 90 | Adeh_0548 | Anaeromyxobacter dehalogenans | |||
| SAMT0025 | Conserved hypothetical protein | 38 | 100 | SCO7248 | Streptomyces coelicolor | |||
| SAMT0026 | Putative phosphotransferase | 54 | 91 | ard | Streptomyces avermitilis | |||
| SAMT0027 | Unknown | |||||||
| SAMT0028 | Putative secreted protein | 47 | 80 | SCO0072 | Streptomyces coelicolor | |||
| SAMT0029 | Putative secreted protein | 61 | 89 | SCO0072 | Streptomyces coelicolor | |||
| SAMT0030 | Unknown | 30 | 67 | Francci3_0808 | Frankia sp. strain CcI3 | |||
| SAMT0031 | Unknown | |||||||
| SAMT0032 | Putative truncated transposase | 71 | 80 | orf118 | pSLA2-L | Streptomyces rochei | ||
| SAMT0033 | Putative secreted protein | 58 | 97 | SCO0072 | Streptomyces coelicolor | |||
| SAMT0034 | Putative secreted protein | 86 | 100 | SCO0072 | Streptomyces coelicolor | |||
| SAMT0035 | Conserved hypothetical protein | 60 | 100 | SCO0073 | Streptomyces coelicolor | |||
| SAMT0036 | Putative SAM-dependent methyltransferase | 67 | 98 | SCO2653 | Streptomyces coelicolor | |||
| SAMT0037 | Conserved hypothetical protein | 82 | 100 | SCO0031 | Streptomyces coelicolor | |||
| SAMT0038 | Putative transmembrane restriction endonuclease | 87 | 100 | SCO7763 | Streptomyces coelicolor | |||
| SAMT0039 | Unknown | |||||||
| SAMT0040 | Putative stress response protein | 77 | 100 | SCO3763 | Streptomyces coelicolor | |||
| SAMT0041 | Unknown | 54 | 48 | Francci3_1126 | Frankia sp. strain CcI3 | |||
| SAMT0042 | Putative membrane protein | 37 | 100 | SAV3190 | Streptomyces avermitilis | |||
| SAMT0043 | Unknown | |||||||
| SAMT0044 | Putative regulator | 39 | 81 | SAV1103 | Streptomyces avermitilis | |||
| SAMT0045 | Putative anti-sigma factor antagonist (pseudogene) | 42 | 81 | SCO3692 | Streptomyces coelicolor | |||
| SAMT0046 | Putative regulator | 71 | 96 | prpC3 | Streptomyces avermitilis | |||
| SAMT0047 | Putative hydrolase | 79 | 100 | SAV923 | Streptomyces avermitilis | |||
| SAMT0048 | Putative urease beta/gamma subunit | 50 | 94 | DR_A0319 | Deinococcus radiodurans | |||
| SAMT0049 | Putative urease alpha subunit | 65 | 98 | SCO1234 | Streptomyces coelicolor | |||
| SAMT0050 | Putative ureF-like urease accessory protein | 76 | 100 | ureF | Streptomyces avermitilis | |||
| SAMT0051 | Putative ureG-like urease accessory protein | 75 | 98 | ureG | Streptomyces avermitilis | |||
| SAMT0052 | Putative ureD-like urease accessory protein | 54 | 81 | SCO1231 | Streptomyces coelicolor | |||
| c | SAMT0065 | Putative truncated transposase | 41 | 100 | SAV18 | Streptomyces avermitilis | ||
| SAMT0066 | Putative haloacid dehalogenase | 89 | 99 | SAV737 | Streptomyces avermitilis | |||
| d | SAMT0071 | Putative transcriptional regulator | 41 | 96 | Saccharopolyspora erythraea | |||
| SAMT0072 | Putative esterase | 38 | 100 | SCO4392 | Streptomyces coelicolor |
a
FAD, flavin adenine dinucleotide; BNR, bacterial neuraminidase repeat; ACP, acyl carrier protein; NTP, nucleoside triphosphate.
b
Results for the best BLASTP hit are summarized.
c
“Overlap” corresponds to the ratio between the length of the BLASTP alignment and the length of the query protein (for cases in which this ratio was >100%, 100% overlap was indicated).