CDS 127 - 453 /note=GM and Glimmer suggest the same start. It has better Z and Final scores. CDS 434 - 1993 /note=The suggested start avoids large overlaps. CDS 2034 - 3443 /note=Pham #130463 is associated with the portal protein function on several clusters. CDS 3443 - 4939 /note=High Z-score, Full GM coding capacity. HHPRED shows a 100% match for mu-like prophage protein whereas NCBI shows head maturation protease. CDS 4941 - 5387 /note=The suggested start avoids a large overlap. CDS 5416 - 6348 /note=Best Z and Final scores, and full GM coding capacity. HHPRED shows a high probability with major capsid protein of other known phages. CDS 6345 - 6746 /note=We picked GM suggested start to maximize coding capacity. CDS 6962 - 7354 /note=Better Z and Final scores. Some phages are identifying this function as head-to-tail connector complex protein and we wonder if this is a revised function. CDS 7354 - 7677 /note=Suggested start avoids a major overlap. CDS 7674 - 8060 /note=The start suggested by Glimmer maximizes coding potential. This pham (212533) is related to the tail terminator function among several clusters. CDS 8427 - 8969 /note=The start suggested by Glimmer has better Z and Final scores. CDS 8972 - 9328 /note=This strat avoids a major overlap. CDS 9329 - 9712 /note=The suggested start maximizes coding potential. CDS join(9329..9688,9688..10194) /note=This is a frameshift, and the slippery sequence is on 9688. CDS 10209 - 15176 /note=The suggested start maximizes coding potential. CDS 15181 - 16242 /note=Same sequence length with bacteriophages DumpsterDude and Ruthy. /note=99.4334% identity, 100% alignment and 100% coverage with minor tail protein of Gordonia phage Ruthy CDS 16244 - 17938 /note=Low z-score. 100% coverage with DumpsterDude and Ruthy in NCBI BLAST. CDS 17953 - 18396 /note=All GM coding capacity and same sequence length with Ruthy. 95.9184% identity with minor tail protein, 100% alignment, and 100% coverage with Gordonia phage Ruthy. CDS 18396 - 19496 /note=High Z-Score, all GM coding capacity, equal sequence length with Gordonia phage Ruthy. Identity is 97.2678%, alignment is 98.0874%, and coverage is 100% similar to Ruthy. CDS 19498 - 21270 /note=We favor the Glimmer call for the start, although GM also has good Z and Final scores. CDS 21598 - 22305 /note=GM proposed start increases coding capacity. CDS 22305 - 23216 /note=Both, GM and Glimmer, suggest the same start, that avoids a avoids a major overlap. CDS 23219 - 23686 /note=Same Glimmer and GM start. Best Z and Final scores. CDS 23687 - 23947 /note=Same Glimmer and GM start. Several other phages on different clusters are calling this function a "membrane protein" on NCBI. However, our gene has very low alignment and identity with those phages. CDS 24514 - 25320 /note=Glimmer start was favored because it increases coding capacity. CDS 25328 - 27967 /note=Glimmer suggested start avoids some overlap and maximizes coding capacity. This is a orphan pham, and on NCBI BLAST the alignment and identity are very low with other phages that are calling this function a hydrolase. /note=DNA Master has a BLAST for SGNH/GDSL hydrolase family protein (Gordonia sp UBA 6683) showing a 97.4% alignment, 40.9% identity, and 58.8% similarity. CDS 28020 - 28286 /note=Another orphan pham, with low hits on all databases. This gene was deleted because overlaps with a reverse gene. CDS 28634 - 29137 /note=This genes has a hit on Deep TMHMM. CDS complement (29103 - 29222) /note=Just Glimmer suggest a start. Another orphan pham. When the sequenced was blasted on NCBI, the hit is Gordonia phage Bradissa, with identity of 87%. CDS complement (29378 - 30640) /note=Same Glimmer and GM start. Full GM coding capacity and E-value at 0 CDS 30835 - 31752 /note=Glimmer suggested start had better Z and Final scores. CDS complement (33075 - 34244) /note=Same Glimmer and GM suggested startNeither the Final or the Z scores are great. CDS complement (34258 - 34485) /note=Both Glimmer and GM suggest the chosen start, which avoids a gap and overlap. CDS complement (34631 - 35044) /note=Same Glimmer and GM start does not have the best scores but maximizes coding potential. CDS complement (35109 - 35753) /note=Same Glimmer and GM start with high final scores. The hit on identity and alignment on NCBI is relatively low (68.4 and 674.4 respectively). CDS 36013 - 36261 /note=Both Glimmer and GM call the selected start. However, the start 35980 has equal Final and Z acores and could maximize coding potential. CDS 36606 - 37415 /note=Both Glimmer and GM suggest the chosen start. It also has the best Z and Final scores. CDS 37412 - 37723 /note=The chosen start is uggested by Glimmer and GM, and it has the best Z and final scores. CDS 37720 - 37932 /note=The chosen strat avoids a major overlap. CDS 38018 - 38356 /note=Best Z and final scores. CDS 39232 - 39444 /note=hypothetical protein aligned with BaxterFox CDS 39763 - 40095 /note=The phages Ruthy and Dumpsterdude have a hit for tail fiber protein on NCBI, but Phagesdb blast is showing NKF. CDS 40092 - 41021 /note=The chosen strat is suggested by Glimmer and GM. CDS 41018 - 42052 /note=Glimmer and GM suggest the selected start. It maximizes coding potential. CDS 42045 - 42518 /note=Glimmer ang GM suggest the selected start. It avoids a 78 bp overlap and a 148 bp gap. CDS 42694 - 42951 /note=This is an orphan pham. CDS 42948 - 43190 /note=Just one hit on NCBI. CDS 43561 - 43887 /note=Low identity and alignment on NCBI. CDS 43868 - 45436 /note=Glimmer and Gm suggest the chosen strat. It avoids an overlap and a gap. CDS 45436 - 45627 /note=There is no evidence for the "DNA methyltransferase" function on toher phages of the DW cluster. However, the pham 6265 is listed as having the mentioned function. CDS 45888 - 46604 /note=High z-score. Phagesdb BLAST shows similarity to phages Ruthy and DumpsterDude. NCBI BLAST shows 98% coverage with Gordonia phages Ruthy and DumpsterDude, however % identity is low. CDS 46601 - 46876 /note=Full GM coding capacity. Strong coverage with Gordonia phage Malibo for helix-turn-helix DNA binding domain protein. Moderate identity and alignment with Malibo. CDS 46873 - 47409 /note=High z-score. Phagesdb BLAST shows similarity to Pipp and Melba with DNA Methylase. NCBI BLAST shows 100% coverage for both Gordonia phage Melba and Pipp. CDS 48177 - 48563 /note=Full GM coding capacity. Similar to RNA polymerase sigma factor Gordonia phage Vasanti, also identified as DNA binding protein. No HTH confirmed. CDS 48544 - 49545 /note=Full GM coding capacity. Strong evidence to Gordonia phage Ruthy replication initiation protein and helix-turn-helix DNA-binding domain protein. CDS 49542 - 49913 /note=Full GM coding capacity. Evidence shows it resembles RusA-like Holliday junction resolvase Gordonia phage Ruthy and DumpsterDude. CDS 49910 - 50791 /note=Full GM Coding Capacity and high Z-Score. Strong evidence suggests that Ruthy is similar for a helix-turn-helix DNA-binding domain protein. CDS 50880 - 51233 /note=Strong evidence with HNH endonuclease from the Gordonia phage Ruthy and DumpsterDude. Full GM coding capacity CDS 51395 - 51649 /note=Full GM coding capacity. Strong evidence with Gordonia phage Ruthy which encodes for a hypothetical protein.