TABLE 2.
Predicted ORFs found in the RSA1 genome
| Coding sequence | Position (5′ to 3′) | G+C content (%) | Protein length (aa) | Mol. mass (Da) | Amino acid sequence identity/similarity to best homologs | BLAST score (E value) | Accession no. |
|---|---|---|---|---|---|---|---|
| ORF1 | 353-742 | 65.9 | 130 | 13,173 | Janthinobacterium lividum hypothetical protein | 113 (3e-24) | A1X1P8 |
| PAAR motif protein (Burkholderia multivorans) | 82 (1e-14) | A0UPR0 | |||||
| ORF2 | 747-1247 | 68.9 | 167 | 18,701 | Janthinobacterium lividum hypothetical protein | 168 (8e-41) | A1X1P7 |
| ORF3 | 1260-2189 | 68.1 | 310 | 33,466 | Burkholderia thailandensis hypothetical protein | 79 (3e-13) | Q2SWS5 |
| ORF4 | 2102-2914 | 65.5 | 271 | 30,022 | Janthinobacterium lividum hypothetical protein | 176 (1e-42) | A1X1P4 |
| ORF5 | 4008-2905 | 65.4 | 368 | 41,541 | Bacteriophage protein RSc1941 | 642 (0.0) | Q8XY22 |
| Bacteriophage P2 gpQ probable capsid portal protein | 396 (e-109) | P25480 | |||||
| ORF6 | 5786-4008 | 65.3 | 593 | 67,089 | Terminase RSc1939 (ATPase subunit-related protein) | 707 (0.0) | Q8XY24 |
| Putative ATPase subunit of terminase (gpP) | 504 (e-141) | Q8Z358 | |||||
| Bacteriophage P2 gpP | 431 (e-119) | P25479 | |||||
| ORF7 | 5922-6764 | 65.2 | 281 | 30,415 | Bacteriophage protein RSc1938 | 461 (e-128) | Q8XY25 |
| Phage capsid scaffolding protein (gpO) | 201 (4e-50) | Q2T5K2 | |||||
| Bacteriophage P2 gpO | 192 (2e-47) | P25478 | |||||
| ORF8 | 6821-7837 | 63.5 | 339 | 37,784 | Bacteriophage protein RSc1937 | 537 (e-151) | Q8XY26 |
| P2 family phage major capsid protein (gpN) | 382 (e-104) | Q45YE6 | |||||
| Bacteriophage P2 gpN | 346 (8e-94) | P25477 | |||||
| ORF9 | 7837-8556 | 68.0 | 240 | 26,476 | Bacteriophage protein RSc1936 | 439 (e-122) | Q8XY27 |
| Terminase, endonuclease subunit (gpM) | 180 (5e-44) | P25476 | |||||
| ORF10 | 8656-9132 | 70.0 | 159 | 17,076 | Bacteriophage protein RSc1935 | 322 (5e-87) | Q8XY28 |
| Head completion/stabilization protein L (gpL) | 120 (3e-26) | P25475 | |||||
| ORF11 | 9135-9338 | 72.1 | 68 | 7,307 | Bacteriophage protein RSc1934 | 138 (1e-31) | Q8XY29 |
| Phage tail X (gpX) | 91 (2e-17) | Q41S37 | |||||
| ORF12 | 9357-9758 | 70.6 | 134 | 13,018 | Phage-related transmembrane protein RSc1933 | 179 (5e-44) | Q8XY30 |
| ORF13 | 9758-10069 | 70.7 | 104 | 11,253 | Phage-related transmembrane protein RSc1932 | 173 (3e-42) | Q8XY31 |
| Putative holin | 50 (3e-05) | A1AE02 | |||||
| ORF14 | 10069-10872 | 70.1 | 268 | 28,697 | Phage-related protein (hydrolase) RSc1931 | 500 (e-140) | Q8XY32 |
| Phage-encoded peptidoglycan-binding protein | 290 (5e-77) | A0UZD9 | |||||
| Bacteriophage φCTX ORF11 | 249 (8e-65) | Q92XL6 | |||||
| ORF15 | 10872-11366 | 67.5 | 165 | 17,049 | Signal peptide protein RSc1930 | 169 (6e-41) | Q8XY33 |
| ORF16 | 11366-11797 | 67.4 | 144 | 16,042 | Tail completion-like protein RSc1929 | 286 (2e-76) | Q8XY34 |
| Bacteriophage P2 gpR | 126 (3e-28) | P36933 | |||||
| ORF17 | 11797-12240 | 68.0 | 148 | 16,679 | Tail completion-like protein RSc1928 | 170 (2e-41) | Q8XY35 |
| Bacteriophage P2 tail completion protein gpS | 67 (4e-10) | P36934 | |||||
| ORF18 | 13153-12215 | 45.6 | 313 | 36,444 | Burkholderia pseudomallei hypothetical protein | 189 (1e-46) | Q6S459 |
| ORF19 | 13397-14011 | 69.2 | 205 | 21,753 | Phage-related protein RSc1925 (baseplate assembly-like protein) | 384 (e-105) | Q8XY38 |
| Baseplate assembly protein V (gpV) | 160 (3e-38) | A0UFJ5 | |||||
| Bacteriophage P2 gpV | 108 (2e-22) | P31340 | |||||
| ORF20 | 14011-14355 | 69.4 | 115 | 12,612 | Phage-related protein RSc1924 (baseplate assembly-like protein) | 216 (3e-55) | Q8XY39 |
| gpW/gp25 family protein | 124 (1e-27) | A0U2D3 | |||||
| Bacteriophage P2 gpW | 89 (9e-17) | P51768 | |||||
| ORF21 | 14361-15266 | 69.8 | 302 | 32,456 | Baseplate assembly-like protein RSc1923 | 517 (e-145) | Q8XY40 |
| Baseplate J-like protein (gpJ) | 320 (8e-86) | Q1QXR7 | |||||
| Bacteriophage P2 gpJ | 317 (5e-85) | P51767 | |||||
| ORF22 | 15262-15876 | 70.4 | 205 | 22,168 | Tail-related protein RSc1922 | 370 (e-101) | Q8XY41 |
| Phage tail protein gpI (tail formation-like protein) | 227 (2e-58) | Q1QXR8 | |||||
| Bacteriophage P2 gpI | 216 (4e-55) | P26701 | |||||
| ORF23 | 15884-17545 | 70.8 | 554 | 57,813 | Tail fiber-related protein RSc1921 | 951 (0.0) | Q8XY42 |
| Tail fiber protein gpH | 269 (3e-70) | Q87ZM6 | |||||
| Bacteriophage P2 gpH | 148 (9e-34) | P26700 | |||||
| ORF24 | 16871-17545 | 67.8 | 225 | 23,947 | Phage tail fiber protein RSc1692 | 108 (2e-22) | Q8XYR6 |
| ORF25 | 17561-18310 | 72.8 | 250 | 25,888 | Tail fiber assembly-like protein RSc1920 | 362 (7e-99) | Q8XY43 |
| ORF26 | 18310-18771 | 68.8 | 154 | 17,140 | Hypothetical protein RSc1919 | 259 (2e-68) | Q8XY44 |
| ORF27 | 18868-20040 | 67.7 | 391 | 42,397 | Phage-related tail sheath protein RSc1918 | 758 (0.0) | Q8XY45 |
| P2 major tail sheath protein gpFI | 585 (e-165) | Q66BD0 | |||||
| Bacteriophage P2 gpFI | 510 (e-143) | P22501 | |||||
| ORF28 | 20075-20581 | 62.5 | 169 | 18,802 | Phage-related protein (major tail protein) RSc1917 | 341 (7e-93) | Q8XY46 |
| Putative P2 tail tube protein gpFII | 174 (1e-42) | Q66BD1 | |||||
| Bacteriophage P2 gpFII | 147 (2e-34) | P22502 | |||||
| ORF29 | 20630-20983 | 63.2 | 118 | 12,796 | Phage-related protein RSc1916 | 225 (5e-58) | Q8XY47 |
| Bacteriophage P2 gpE | 83 (5e-15) | Q66BM8 | |||||
| ORF30 | 21081-23657 | 69.6 | 859 | 90,965 | Phage-related tail transmembrane protein RSc1914 | 1,280 (0.0) | Q8XY49 |
| Bacteriophage P2 tail protein gpT | 109 (6e-22) | Q66BN0 | |||||
| ORF31 | 23749-24168 | 65.2 | 140 | 15,695 | Phage-related tail protein RSc1913 | 281 (7e-75) | Q8XY50 |
| Bacteriophage P2 gpU | 155 (5e-37) | Q41SZ1 | |||||
| ORF32 | 24168-25370 | 66.2 | 401 | 43,433 | Phage related protein RSc1912 | 669 (0.0) | Q8XY51 |
| Bacteriophage P2 gpD | 322 (3e-86) | Q66BD6 | |||||
| ORF33 | 26135-25392 | 61.8 | 248 | 26,462 | Hypothetical transmembrane protein | 134 (4e-30) | Q8XSE3 |
| ORF34 | 27434-26217 | 62.6 | 406 | 47,730 | Transposase ISRSO15 | 803 (0.0) | Q8XFK1 |
| ORF35 | 28022-27609 | 59.9 | 138 | 15,091 | XRE family, transcriptional regulator | 103 (2e-21) | A0UFH8 |
| Putative phage DNA-binding protein | 102 (6e-21) | Q63YP6 | |||||
| DNA-binding repressor RSc1907 | 99 (7e-20) | Q8XY56 | |||||
| ORF36 | 28062-28490 | 59.7 | 143 | 15,823 | Unknown | ||
| ORF37 | 28539-28730 | 58.3 | 64 | 7,380 | Unknown | ||
| ORF38 | 28730-28975 | 66.5 | 82 | 9,126 | Putative transcription activator RSc1904 | 124 (2e-27) | Q8XY59 |
| Phage transcription activator Ogr/Delta | 77 (4e-13) | A0UFH5 | |||||
| ORF39 | 29093-29644 | 65.9 | 184 | 20,512 | Hypothetical phage protein | 235 (9e-61) | Q63YQ0 |
| Prophage antirepressor | 95 (1e-18) | Q3R0Y7 | |||||
| ORF40 | 29657-29887 | 61.9 | 77 | 8,082 | Hypothetical protein RSc1903 | 75 (1e-12) | Q8XY60 |
| ORF41 | 29887-30048 | 65.8 | 54 | 5,540 | Hypothetical protein RSc1902 | 81 (1e-14) | Q8XY61 |
| ORF42 | 30048-30251 | 63.4 | 68 | 7,171 | Transmembrane protein RSc1901 | 58 (2e-07) | Q8XY62 |
| ORF43 | 30254-30487 | 64.5 | 78 | 8,612 | Transmembrane protein Rsc1900 | 147 (2e-34) | Q8XY63 |
| ORF44 | 30483-30692 | 70.0 | 70 | 7,810 | Hypothetical protein RSc1899 | 103 (3e-21) | Q8XY64 |
| ORF45 | 30770-31243 | 65.5 | 158 | 17,212 | Unknown | ||
| ORF46 | 31512-31799 | 65.3 | 96 | 11,432 | Pseudomonas resinovorans/pCAR1 ORF80 | 128 (1e-28) | Q8GHW9 |
| ORF47 | 31802-34603 | 65.6 | 934 | 103,175 | Zinc finger, CHC family protein | 1,454 (0.0) | A0UFH0 |
| φ52237 hypothetical protein (AAZ72605.1) | 1437 (0.0) | Q45Y14 | |||||
| Conserved hypothetical phage protein | 1,433 (0.0) | Q63YQ8 | |||||
| ORF48 | 33589-31811 | 66.4 | 593 | 63,364 | Hypothetical protein φ52237 (AAZ72604.1) | 332 (1e-80) | Q45Y15 |
| ORF49 | 34778-35494 | 61.7 | 239 | 25,241 | Unknown | ||
| ORF50 | 35709-36788 | 64.3 | 360 | 41,524 | Site-specific recombinase, phage integrase | 514 (e-144) | Q62FM0 |
| tRNA | 36831-36875 | 71.1 | attP [Arg tRNA(CCG)] R. solanacearum GMI1000 chromosomal sequence | 90 (7e-17) | AL646073 | ||
| ORF51 | 37124-38182 | 56.4 | 353 | 38,895 | Unknown |