| Detailed Information for Phage Optimus | |
| Discovery Information | |
| Isolation Host | Mycobacterium smegmatis mc²155 |
| Found By | Taylor Mann |
| Year Found | 2010 |
| Location Found | Holland, MI USA |
| Finding Institution | Hope College |
| Program | Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science |
| From enriched soil sample? | No |
| Isolation Temperature | 37°C |
| GPS Coordinates | 42.7895 N, 86.100953 W Map |
| Discovery Notes | Optimus was found under approximately 8 cm of moist soil and decaying wood-chips. This soil was underneath a tree and about 2 feet away from a pedestrian sidewalk. The temperature was 24.4 degrees Celsius when collected. |
| Sequencing Information | |
| Sequencing Complete? | Yes |
| Date Sequencing Completed | Jan 27, 2011 |
| Genome length (bp) | 109270 |
| Character of genome ends | 3' Sticky Overhang |
| Overhang Length | 4 bases |
| Overhang Sequence | ATCC |
| GC Content | 60.8% |
| Fasta file available? | Yes: Download fasta file |
| Characterization | |
| Cluster | J |
| Subcluster | -- |
| Cluster Life Cycle | Temperate |
| Other Cluster Members |
Click to ViewAriel Bagrid BAKA Beem Bobby Bombitas Constella Courthouse Dallas DmpstrDiver Dove Duke13 Ejimix EricMillard Gonephishing Halley Hannaconda HokkenD Hughesyang JuicyJay Kalah2 KashFlow Klein LittleE Lucky2013 MiaZeal Minerva NihilNomen Odette Omega Optimus Phoebus Porcelain Pound Redno2 Schatzie Squint Superphikiman Thibault ThreeRngTarjay Wanda Yeet Zelink |
| Annotating Institution | Unknown or unassigned |
| Annotation Status | In GenBank |
| Plaque Notes | After 24 hours of incubation at 37°C, the average plaque size was 1.325 mm. After 48 hours of incubation the average size varied depending on the density of phage. For phage with ample room to grow (less then approximately 350 plaque forming units), the average size was 4.76 mm. Plates that contained more then approximately 350 plaques were too difficult to measure because they ran into each other. After 72 hours of incubation with ample room to grow plaques grew to an average of 6.2 mm. After 72 hours of incubation Optimus ceased growth. The morphology of phage Optimus was very consistent once variations due to plaque density were accounted for. After 24 hours, a clear center was visible with a turbid area around that clear center, but the edges were not clearly defined. Furthermore, plaques near the edge of the plate had an oblong shape, resembling a comet tail. This comet tail always faced the edge of the plate while the clear center was closest to the middle of the plate. After 48 hours of incubation at 37°C not only was there a growth in plaque size, but there was also a more defined morphology. The edges of both the clear center and the turbid outer ring were more definite. Growth occurred in the turbid outer ring while the size of the clear center remained the same. The comet tail and clear center remain altered towards the edge and middle of the plate, respectively. Additionally, a higher concentration of bacteria surrounding the plaque was suggested by the lighter, more concentrated color. As the plaques grew in size, the relatively vague halo of bacteria concentration increases as suggested by the lighter coloration becoming more noticeable with the increase in plaque size. After 72 hours of incubation there was a slightly altered morphology, and an increase in bacteria surrounding the plaque as indicated by a lighter, more concentrated color. Under certain concentrations, around 250 plaques, the plaques formed another defined ring. The plaque morphology still contains a small clear center with a turbid ring and the comet tail effect; however, at 72 hours there were two additional rings on the outside of the original clear center and thick turbid ring. The first of these additional rings was more turbid then the second. In smaller plaque concentrations this last ring was faintly visible, but its edges were not as defined as those found in higher concentrations. Plates with more then approximately 300 plaques ran into each other after 72 hours so this morphology did not develop. After 72 hours of incubation, size and morphology of Optimus remain constant. |
| Morphotype | Siphoviridae |
| Number of Genes | 230 |
| Number of tRNAs | 1 |
| Number of tmRNAs | 0 |
| Has been Phamerated? | Yes |
| Gene List |
Click to ViewOptimus_1 Optimus_2 Optimus_3 Optimus_4 Optimus_5 Optimus_6 Optimus_7 Optimus_8 Optimus_9 Optimus_10 Optimus_11 Optimus_12 Optimus_13 Optimus_14 Optimus_15 Optimus_16 Optimus_17 Optimus_18 Optimus_19 Optimus_20 Optimus_21 Optimus_22 Optimus_23 Optimus_24 Optimus_25 Optimus_26 Optimus_27 Optimus_28 Optimus_29 Optimus_30 Optimus_31 Optimus_32 Optimus_33 Optimus_34 Optimus_35 Optimus_36 Optimus_37 Optimus_38 Optimus_39 Optimus_40 Optimus_41 Optimus_42 Optimus_43 Optimus_44 Optimus_45 Optimus_46 Optimus_47 Optimus_48 Optimus_49 Optimus_50 Optimus_51 Optimus_52 Optimus_53 Optimus_54 Optimus_55 Optimus_56 Optimus_57 Optimus_58 Optimus_59 Optimus_60 Optimus_61 Optimus_62 Optimus_63 Optimus_64 Optimus_65 Optimus_66 Optimus_67 Optimus_68 Optimus_69 Optimus_70 Optimus_71 Optimus_72 Optimus_73 Optimus_74 Optimus_75 Optimus_76 Optimus_77 Optimus_78 Optimus_79 Optimus_80 Optimus_81 Optimus_82 Optimus_83 Optimus_84 Optimus_85 Optimus_86 Optimus_87 Optimus_88 Optimus_89 Optimus_90 Optimus_91 Optimus_92 Optimus_93 Optimus_94 Optimus_95 Optimus_96 Optimus_97 Optimus_98 Optimus_99 Optimus_100 Optimus_101 Optimus_102 Optimus_103 Optimus_104 Optimus_105 Optimus_106 Optimus_107 Optimus_108 Optimus_109 Optimus_110 Optimus_111 Optimus_112 Optimus_113 Optimus_114 Optimus_115 Optimus_116 Optimus_117 Optimus_118 Optimus_119 Optimus_120 Optimus_121 Optimus_122 Optimus_123 Optimus_124 Optimus_125 Optimus_126 Optimus_127 Optimus_128 Optimus_129 Optimus_130 Optimus_131 Optimus_132 Optimus_133 Optimus_134 Optimus_135 Optimus_136 Optimus_137 Optimus_138 Optimus_139 Optimus_140 Optimus_141 Optimus_142 Optimus_143 Optimus_144 Optimus_145 Optimus_146 Optimus_147 Optimus_148 Optimus_149 Optimus_150 Optimus_151 Optimus_152 Optimus_153 Optimus_154 Optimus_155 Optimus_156 Optimus_157 Optimus_158 Optimus_159 Optimus_160 Optimus_161 Optimus_162 Optimus_163 Optimus_164 Optimus_165 Optimus_166 Optimus_167 Optimus_168 Optimus_169 Optimus_170 Optimus_171 Optimus_172 Optimus_173 Optimus_174 Optimus_175 Optimus_176 Optimus_177 Optimus_178 Optimus_179 Optimus_180 Optimus_181 Optimus_182 — tRNA Optimus_183 Optimus_184 Optimus_185 Optimus_186 Optimus_187 Optimus_188 Optimus_189 Optimus_190 Optimus_191 Optimus_192 Optimus_193 Optimus_194 Optimus_195 Optimus_196 Optimus_197 Optimus_198 Optimus_199 Optimus_200 Optimus_201 Optimus_202 Optimus_203 Optimus_204 Optimus_205 Optimus_206 Optimus_207 Optimus_208 Optimus_209 Optimus_210 Optimus_211 Optimus_212 Optimus_213 Optimus_214 Optimus_215 Optimus_216 Optimus_217 Optimus_218 Optimus_219 Optimus_220 Optimus_221 Optimus_222 Optimus_223 Optimus_224 Optimus_225 Optimus_226 Optimus_227 Optimus_228 Optimus_229 Optimus_230 Optimus_231 |
| Publication Info | |
| Uploaded to GenBank? | Yes |
| GenBank Accession | JF957059 |
| Refseq Number | None yet |
| Published in Paper | Pope, Bowman, Russell, et al 2015, eLIFE: Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity |
| Archiving Info | |
| Archiving status | Archived |
| Pitt Freezer Box# | 2 |
| Pitt Freezer Box Grid# | E8 |
| Available Files | |
| Plaque Picture | Download |
| Restriction Digest Picture | Download |
| EM Picture | Download |
