CDS 43 - 348
  /gene="1"
  /product="gp1"
  /function="hypothetical protein"
  /locus tag="Sourignavong_1"
    /note=Original Glimmer call @bp 43 has strength 8.77
    /note=SSC: 43-348 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein SEA_DECURRO_1 [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 1.32843E-63 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.485, -2.0949393225970705, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DECURRO_1 [Arthrobacter phage Decurro] ],,YP_009191294,100.0,1.32843E-63 SIF-HHPRED:  SIF-Syn: synteny with other AN phages
    /note=there are no good matches based e-values from BLAST or HHPRED. no predicted TM domains

CDS 345 - 560
  /gene="2"
  /product="gp2"
  /function="hypothetical protein"
  /locus tag="Sourignavong_2"
    /note=Original Glimmer call @bp 345 has strength 7.38; Genemark calls start at 345
    /note=SSC: 345-560 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LINK_2 [Arthrobacter phage Link]],,NCBI, q1:s1 100.0% 1.82324E-43 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.733, -5.544323445864165, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LINK_2 [Arthrobacter phage Link]],,ASR83562,100.0,1.82324E-43 SIF-HHPRED: GT28_MurG; undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase.,,,cd03785,67.6056,81.8 SIF-Syn: synteny with other AN phages
    /note=no good matches based e-values from BLAST or HHPRED; no predicted TM domains

CDS 557 - 664
  /gene="3"
  /product="gp3"
  /function="hypothetical protein"
  /locus tag="Sourignavong_3"
    /note=Original Glimmer call @bp 548 has strength 8.9
    /note=SSC: 557-664 CP: yes SCS: glimmer-cs ST: SS BLAST-Start: [hypothetical protein SEA_LAILA_3 [Arthrobacter phage Laila]],,NCBI, q1:s1 91.4286% 5.51421E-8 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.434, -4.93147019740927, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LAILA_3 [Arthrobacter phage Laila]],,QDB74327,96.9697,5.51421E-8 SIF-HHPRED: Hol_Tox ; Putative Holin-like Toxin (Hol-Tox),,,PF16935.9,97.1429,86.4 SIF-Syn: Synteny with AN phages Laila gene 3 and Seume gene 2
    /note=- There are no known functions for the Phagesdb Function Frequency. The E-values under Phagesdb, HHPRED are not within the guidelines. There is no known function for all genes under NCBI Blast.
    /note=- There is an interesting few hits in HHPRED for a toxin related gene, but without stronger evalues or additional evidence did not call this function

CDS 725 - 907
  /gene="4"
  /product="gp4"
  /function="hypothetical protein"
  /locus tag="Sourignavong_4"
    /note=Original Glimmer call @bp 725 has strength 7.31; Genemark calls start at 749
    /note=SSC: 725-907 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_DECURRO_3 [Arthrobacter phage Decurro] ],,NCBI, q3:s12 96.6667% 4.91214E-30 GAP: 60 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.624, -4.955328222098073, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DECURRO_3 [Arthrobacter phage Decurro] ],,YP_009191296,78.8732,4.91214E-30 SIF-HHPRED: DUF2883 ; Protein of unknown function (DUF2883),,,PF11097.12,43.3333,28.7 SIF-Syn: Synteny with other AN phages genes 3 or 4
    /note=Function unknown based on HHpred, Phagesdb Blast, and NCBI Blast.

CDS 901 - 2391
  /gene="5"
  /product="gp5"
  /function="terminase"
  /locus tag="Sourignavong_5"
    /note=Original Glimmer call @bp 901 has strength 9.97; Genemark calls start at 901
    /note=SSC: 901-2391 CP: no SCS: both ST: SS BLAST-Start: [terminase [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 0.0 GAP: -7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.178, -2.700465369687878, yes F: terminase SIF-BLAST: ,,[terminase [Arthrobacter phage Decurro] ],,YP_009191297,100.0,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,91.7339,100.0 SIF-Syn: Yes with Decurro
    /note=terminase is the found function based on other genetically similar phages on Phagesdb BLAST, with an e-value of 0 we can be confident in the function.

CDS 2393 - 2596
  /gene="6"
  /product="gp6"
  /function="hypothetical protein"
  /locus tag="Sourignavong_6"
    /note=Original Glimmer call @bp 2393 has strength 7.31; Genemark calls start at 2393
    /note=SSC: 2393-2596 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JESSICA_6 [Arthrobacter phage Jessica] ],,NCBI, q1:s1 100.0% 1.47306E-40 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.532, -3.8308929311341546, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_JESSICA_6 [Arthrobacter phage Jessica] ],,ALF00761,100.0,1.47306E-40 SIF-HHPRED: DUF1059 ; Protein of unknown function (DUF1059),,,PF06348.15,49.2537,90.3 SIF-Syn: Synteny with other AN phages.
    /note=Start determination: Genemark and Glimmer Start chose start at 2393 bp. While start 2540 bp has a better z-score and final score, I chose to agree with the start at 2393. PhagesDB lists the length as 204 bp, which can only agree with the start being 2393, aswell as Pham Staterator has the start listed at 2393 aswell.
    /note=Function determination: Function unknown according to HHpred, Phagesdb Blast, and NCBI Blast. E-values are too large and abdormal.

CDS 2648 - 3808
  /gene="7"
  /product="gp7"
  /function="portal protein"
  /locus tag="Sourignavong_7"
    /note=Original Glimmer call @bp 2648 has strength 7.19; Genemark calls start at 2648
    /note=SSC: 2648-3808 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 0.0 GAP: 51 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.086, -2.8030814177649614, no F: portal protein SIF-BLAST: ,,[portal protein [Arthrobacter phage Decurro] ],,YP_009191299,100.0,0.0 SIF-HHPRED: Portal protein; Prohead I, icosahedral symmetry, HK97, phage, capsid, VIRUS; 3.6A {Escherichia phage HK97},,,8FQL_L,84.456,100.0 SIF-Syn: High levels of synteny with other AN phages
    /note=Similar genes suggest this as a possible portal protein. E-value (0) from Phagesdb BLAST and NCBI BLAST supports this. HHPRED has an e-value of 1.5e-37.

CDS 3805 - 5388
  /gene="8"
  /product="gp8"
  /function="major capsid and protease fusion protein"
  /locus tag="Sourignavong_8"
    /note=Original Glimmer call @bp 3805 has strength 6.81; Genemark calls start at 3805
    /note=SSC: 3805-5388 CP: yes SCS: both ST: SS BLAST-Start: [major head protein [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.101, -4.759312672633257, no F: major capsid and protease fusion protein SIF-BLAST: ,,[major head protein [Arthrobacter phage Decurro] ],,YP_009191300,100.0,0.0 SIF-HHPRED: MAJOR CAPSID PROTEIN; VIRUS, VIRUS COAT PROTEIN, VIRUS/VIRAL PROTEIN, BACTERIOPHAGE, CAPSID, AUTO- CATALYTIC CROSS-LINK, ICOSAHEDRAL VIRUS; 3.45A {BACTERIOPHAGE HK97} SCOP: d.183.1.1,,,1OHG_D,50.2846,99.9 SIF-Syn: Gene 7 in Link has synteny with gene 8 in sourignavong.
    /note=Phases DB Blast supports this function with an e-value of 0.
    /note=HHPRED supports this function with an e-value of 1.1e-23.
    /note=NCBI Blast supports this with an e-value of 0 and %coverage of 100.

CDS 5392 - 5748
  /gene="9"
  /product="gp9"
  /function="head-to-tail adaptor"
  /locus tag="Sourignavong_9"
    /note=Original Glimmer call @bp 5392 has strength 9.63; Genemark calls start at 5392
    /note=SSC: 5392-5748 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail adaptor [Arthrobacter phage Jessica] ],,NCBI, q1:s1 100.0% 3.56244E-78 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.138, -5.5135751627127005, no F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Arthrobacter phage Jessica] ],,ALF00764,100.0,3.56244E-78 SIF-HHPRED: Phage_connect_1 ; Phage gp6-like head-tail connector protein,,,PF05135.17,93.2203,99.5 SIF-Syn: Synteny with Decurro and Link for this gene.
    /note=PhagesDB: A majority of other phages in this cluster with this gene have named its function as head-to tail-adaptor. 
    /note=HHPRED: Top two hits have over 90% coverage and an e value close to 0 (10^-7 or smaller) and name the function as head-to-tail adaptor. Other hits have similar functions. 
    /note=
    /note=Start determination:
    /note= Gene Candidates: Z score is higher than 2, final score is closer to 0. 
    /note=Starterator: 73.2% of other Pham members chose start position 3.
    /note= Gene mark: encompasses coding potential spike.

CDS 5753 - 6109
  /gene="10"
  /product="gp10"
  /function="hypothetical protein"
  /locus tag="Sourignavong_10"
    /note=Original Glimmer call @bp 5762 has strength 7.28; Genemark calls start at 5753
    /note=SSC: 5753-6109 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_DECURRO_9 [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 5.96464E-77 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.754, -4.301170562178417, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DECURRO_9 [Arthrobacter phage Decurro] ],,YP_009191302,100.0,5.96464E-77 SIF-HHPRED:  SIF-Syn: Synteny with other AN phages.
    /note=Looking at phagesDB Blast, all of the related Phages genes in our cluster don`t have a known function, and the supporting E values are all between 1e-60 and 1e-45, providing strong evidence to gene 10 having an unknown function. This function was also supported by looking at HHPRED and NCBI Blast, the lowest E score (.0006) was far to high to support the chosen function of Minor tail protein U, and all NCBI blast results are hypothetical protein which is not a supported function.

CDS 6115 - 6537
  /gene="11"
  /product="gp11"
  /function="major tail protein"
  /locus tag="Sourignavong_11"
    /note=Original Glimmer call @bp 6115 has strength 13.17; Genemark calls start at 6115
    /note=SSC: 6115-6537 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 2.46471E-94 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.561, -3.914968956777623, no F: major tail protein SIF-BLAST: ,,[major tail protein [Arthrobacter phage Decurro] ],,YP_009191303,100.0,2.46471E-94 SIF-HHPRED: Major tail protein; Marine bacteriophage, Cryo-EM, Siphophage, Baseplate, Megatron protein, Tail fibre protein, Distal tail protein, Hub protein, VIRAL; 4.5A {Dinoroseobacter phage vB_DshS-R4C},,,8GTC_F,95.0,99.7 SIF-Syn: Gene 10 Link and Decurro have the same function.
    /note=This function is well supported. E-values are ideal (all less than e-16). Closely related phages have the function of this gene as a major tail protein.
    /note=
    /note=Looking at phagesDB Blast, all of the related Phages genes in our cluster state the function of Major tail protein and the supporting E values are all between 3e-75 and 4e-65, providing strong evidence to gene 11`s function being a Major tail protein. This function was also supported by looking at HHPRED and NCBI Blast, as all E values are idea being less then e-16.

CDS 6537 - 6914
  /gene="12"
  /product="gp12"
  /function="minor tail protein"
  /locus tag="Sourignavong_12"
    /note=Original Glimmer call @bp 6537 has strength 9.95; Genemark calls start at 6537
    /note=SSC: 6537-6914 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 7.38164E-84 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.411, -6.690904047732638, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Decurro] ],,YP_009191304,100.0,7.38164E-84 SIF-HHPRED: Minor_capsid_2 ; Minor capsid protein,,,PF11114.12,68.8,99.5 SIF-Syn: Gene 12 of Sourignavong has synteny with gene 11 of phages Link and Decurro. Gene 11 of both Link and Decurro are minor tail proteins, which supports the function of this gene.
    /note=This function was the only function listed under Phagesdb BLAST other than function unknown and it had a good e-value of 3e-67. NCBI BLAST also lists good e-values for minor tail protein (7.38164e-84). Although there are other functions, such as minor capsid protein listed under HHPRED, the e-values are not as good because the best one is 1.9e-12.

CDS 6921 - 7271
  /gene="13"
  /product="gp13"
  /function="hypothetical protein"
  /locus tag="Sourignavong_13"
    /note=Original Glimmer call @bp 6921 has strength 13.29; Genemark calls start at 6921
    /note=SSC: 6921-7271 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JESSICA_13 [Arthrobacter phage Jessica] ],,NCBI, q1:s1 100.0% 1.68583E-78 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.405, -3.0197905277289068, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_JESSICA_13 [Arthrobacter phage Jessica] ],,ALF00768,100.0,1.68583E-78 SIF-HHPRED: DUF5055 ; Domain of unknown function (DUF5055),,,PF16478.9,68.1034,95.0 SIF-Syn: Synteny with other AN phages
    /note=The e-values for unknown function are very low on Phagedb BLAST and NCBI BLAST.

CDS 7383 - 9380
  /gene="14"
  /product="gp14"
  /function="tape measure protein"
  /locus tag="Sourignavong_14"
    /note=Original Glimmer call @bp 7383 has strength 8.81; Genemark calls start at 7383
    /note=SSC: 7383-9380 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Arthrobacter phage Toulouse] ],,NCBI, q1:s1 100.0% 0.0 GAP: 111 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.27, -4.408951082954879, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Arthrobacter phage Toulouse] ],,ALY10652,100.0,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BF,11.4286,99.9 SIF-Syn: Gene 14 in Sourignavong is in the same location as gene 13 in Decurro and Link.
    /note=When looking at BLAST, many other genomes seemed to match with the function of minor tail protein. These matches had e-values of 0, meaning they show definite correlation in terms of matching. HHPred also showed correlation with a gene in another genome with the same function having an e-value of 4.5e-14.

CDS 9374 - 11191
  /gene="15"
  /product="gp15"
  /function="hypothetical protein"
  /locus tag="Sourignavong_15"
    /note=Original Glimmer call @bp 9374 has strength 10.71; Genemark calls start at 9374
    /note=SSC: 9374-11191 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 0.0 GAP: -7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.036, -2.9008607109931437, no F: hypothetical protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Decurro] ],,YP_009191307,99.8347,0.0 SIF-HHPRED: Tail protein, 43 kDa; tail protein, structural genomics, PSI, MCSG, Protein Structure Initiative, Midwest Center for Structural Genomics, UNKNOWN FUNCTION; 2.1A {Neisseria meningitidis MC58} SCOP: b.106.1.1,,,3D37_A,50.7438,98.1 SIF-Syn: Phamerator displays a good e-values and the high percentage of Synteny between the Sourignavong and the phages Link and  Decurro. These other phages at gene 15 have no function as well.
    /note=No known function has been found as for gene 15 as the Phages db blast list all best options having "no known function" as well as the lowest e-values. Some evidence for being a tail protein from HHPRED, but not strong enough for evidence on its own.

CDS 11196 - 11711
  /gene="16"
  /product="gp16"
  /function="hypothetical protein"
  /locus tag="Sourignavong_16"
    /note=Original Glimmer call @bp 11196 has strength 8.13; Genemark calls start at 11196
    /note=SSC: 11196-11711 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_DECURRO_15 [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 3.22778E-120 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.97, -3.0301037898918786, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DECURRO_15 [Arthrobacter phage Decurro] ],,YP_009191308,100.0,3.22778E-120 SIF-HHPRED: Hypothetical protein; protein-DNA, partition, segregation, parB, DNA BINDING PROTEIN-DNA COMPLEX; HET: EPE, 5IU; 3.0A {Staphylococcus aureus},,,2Q2K_B,9.94152,30.9 SIF-Syn: Phamerator displays good e-values and the high percentage of Synteny between the Sourignavong and the phages Link and  Decurro. These other phages at gene 16 have no function as well.
    /note=In Phages DB Blast there were extremely high e-values (3e-93), but was listed as no function know.There were also good e-values in HHpred and Ncbi blast, but had no function listed . We can then conclude that there is no known function.

CDS 11708 - 12154
  /gene="17"
  /product="gp17"
  /function="lysin A, L-Ala-D-Glu peptidase domain"
  /locus tag="Sourignavong_17"
    /note=Original Glimmer call @bp 11708 has strength 5.85; Genemark calls start at 11714
    /note=SSC: 11708-12154 CP: yes SCS: both-gl ST: SS BLAST-Start: [endolysin, L-Ala-D-Glu peptidase domain [Arthrobacter phage Jessica] ],,NCBI, q1:s1 100.0% 2.00063E-103 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.609, -4.586198330050502, no F: lysin A, L-Ala-D-Glu peptidase domain SIF-BLAST: ,,[endolysin, L-Ala-D-Glu peptidase domain [Arthrobacter phage Jessica] ],,ALF00772,100.0,2.00063E-103 SIF-HHPRED: Peptidase M23; membrane protein, enzyme, TRANSPORT PROTEIN; HET: ADP;{Vibrio cholerae},,,8TZL_E,63.5135,98.5 SIF-Syn: This gene was present in the same location with the same function in both the Link genome and Decurro.
    /note=Phagesdb suggests that this is the function of gene 17 by giving multiple matches within other genomes for this function. Phagesdb BLAST also suggested this as the correct function. All of the given matches had e-values below 10e-7, meaning that were well withing range for this function. To cross reference, we looked at NCBI BLAST and noticed that many of the matches also had a function of endolysin with e-values as low as 2.006e-103.

CDS 12151 - 12792
  /gene="18"
  /product="gp18"
  /function="lysin A, N-acetylmuramoyl-L-alanine amidase domain"
  /locus tag="Sourignavong_18"
    /note=Original Glimmer call @bp 12151 has strength 11.62; Genemark calls start at 12151
    /note=SSC: 12151-12792 CP: yes SCS: both ST: SS BLAST-Start: [amidase [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 2.61055E-158 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.485, -2.0162541296952132, yes F: lysin A, N-acetylmuramoyl-L-alanine amidase domain SIF-BLAST: ,,[amidase [Arthrobacter phage Decurro] ],,YP_009191310,100.0,2.61055E-158 SIF-HHPRED: N-acetylmuramoyl-L-alanine amidase amiD; ZINC AMIDASE, PGRP, Peptidoglycan Recognizing Protein, AmpD, N-ACETYLMURAMYL-L-ALANINE AMIDASE, Cell wall biogenesis/degradation, Hydrolase, Lipoprotein, Membrane, Metal-binding; HET: GOL, AH0; 1.75A {Escherichia coli},,,3D2Y_A,60.0939,99.4 SIF-Syn: Synteny exists between the gene positioned 18th in Sourignavong and the genes in the 17th position for the phages Link, Decurro, and Arby.
    /note=endolysin is a very common function amongst the genetically similar phage genomes

CDS 12798 - 13007
  /gene="19"
  /product="gp19"
  /function="holin"
  /locus tag="Sourignavong_19"
    /note=Original Glimmer call @bp 12798 has strength 2.6
    /note=SSC: 12798-13007 CP: yes SCS: glimmer ST: SS BLAST-Start: [holin [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 7.88712E-40 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.985, -4.2450294671839215, yes F: holin SIF-BLAST: ,,[holin [Arthrobacter phage Decurro] ],,YP_009191311,100.0,7.88712E-40 SIF-HHPRED: Phage_holin_1 ; Bacteriophage holin,,,PF04531.17,92.7536,85.0 SIF-Syn: Gene 19`s location in Sourignavong lines up with Link`s gene 18 in Phamerator.
    /note=PhagesDB BLAST has e-value of 1e-32 showing similar genes have this function.
    /note=
    /note=I agree with the chosen start position and function for Sourignavong gene 19. I have added two pieces of evidence from NCBI BLAST for holin function (e-values of 7.88712e-40 and 2.33302e-37).

CDS 12997 - 13254
  /gene="20"
  /product="gp20"
  /function="hypothetical protein"
  /locus tag="Sourignavong_20"
    /note=Original Glimmer call @bp 12976 has strength 6.81; Genemark calls start at 12976
    /note=SSC: 12997-13254 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_DECURRO_19 [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 1.45382E-53 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.613, -3.670670413150579, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DECURRO_19 [Arthrobacter phage Decurro] ],,YP_009191312,100.0,1.45382E-53 SIF-HHPRED: XhlA ; Haemolysin XhlA,,,PF10779.13,80.0,96.5 SIF-Syn: Gene 20 of Sourignavong has synteny with gene 19 of phages Link and Decurro. Gene 19 of both Link and Decurro do not have a function.
    /note=There was only one function listed under Phagesdb BLAST, and it had a e-value of 8, which is too large. All of the e-values under HHPRED were also too high (the lowest one was 0.13). It only listed hypothetical proteins under NCBI BLAST.
    /note=
    /note=Some evidence from HHPRED for function of `Haemolysin`, but no other supporting evidence.

CDS 13322 - 13576
  /gene="21"
  /product="gp21"
  /function="hypothetical protein"
  /locus tag="Sourignavong_21"
    /note=Original Glimmer call @bp 13322 has strength 8.93; Genemark calls start at 13322
    /note=SSC: 13322-13576 CP: yes SCS: both ST: SS BLAST-Start: [HTH DNA binding protein [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 4.79993E-52 GAP: 67 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.646, -5.654388976111635, no F: hypothetical protein SIF-BLAST: ,,[HTH DNA binding protein [Arthrobacter phage Decurro] ],,YP_009191313,100.0,4.79993E-52 SIF-HHPRED: Uncharacterized protein Rv2667; ClpC2, CymA, N-terminal domain, Transcription factor, DNA BINDING PROTEIN; 1.996A {Mycobacterium tuberculosis H37Rv},,,8ADA_A,47.619,98.8 SIF-Syn: Synteny with other AN phages
    /note=Start Determination: 
    /note=Z-score is closer to 2 than most other candidates. Gap was not too large, and overlap of other candidates was greater than 7bp. The final score of -5.654 is closer to 0 than 8/10 of other gene candidates. Length is over 200, which is optimal for protein coding. 93.2% of genes in the Pham have start position 6. Genemark encompasses all coding potential spike. 
    /note=
    /note=Function: 
    /note=PhagesDB: Most closely related genomes have an unknown function for this gene. 
    /note=HHPRED: Top two hits indicate unknown function.

CDS complement (13573 - 13845)
  /gene="22"
  /product="gp22"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Sourignavong_22"
    /note=Genemark calls start at 13845
    /note=SSC: 13845-13573 CP: yes SCS: genemark ST: SS BLAST-Start: [transcriptional repressor [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 3.05408E-57 GAP: 109 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.287, -8.330202992062844, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[transcriptional repressor [Arthrobacter phage Decurro] ],,YP_009191314,100.0,3.05408E-57 SIF-HHPRED: a.35.1.2 (C:) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]} | CLASS: All alpha proteins, FOLD: lambda repressor-like DNA-binding domains, SUPFAM: lambda repressor-like DNA-binding domains, FAM: Phage repressors,,,SCOP_d3jxbc_,66.6667,98.3 SIF-Syn: Systeny established with gene 21 in both phages  Decurro and Link.
    /note=Start Determination: 
    /note=Gap of 109 is the smallest out of 3 candidates. Lowest spacer score. Gene length is over 200, which is optimal for protein coding. All members of this Pham chose start position 1. Genemark encompasses all of the coding potential spike. 
    /note=
    /note=Function: 
    /note=PhagesDB: Function is top 20 matches, all of which have an optimal e-value. 
    /note=HHPRED: Top hits do not have optimal e value (10^-7) and less than 80% coverage.

CDS 13955 - 14188
  /gene="23"
  /product="gp23"
  /function="helix-turn-helix DNA binding domain, MerR-like"
  /locus tag="Sourignavong_23"
    /note=Original Glimmer call @bp 13955 has strength 5.84; Genemark calls start at 13955
    /note=SSC: 13955-14188 CP: yes SCS: both ST: SS BLAST-Start: [MerR-like helix-turn-helix DNA binding domain protein [Arthrobacter phage Sandman] ],,NCBI, q1:s1 100.0% 2.30235E-47 GAP: 109 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.768, -7.3836251027916555, no F: helix-turn-helix DNA binding domain, MerR-like SIF-BLAST: ,,[MerR-like helix-turn-helix DNA binding domain protein [Arthrobacter phage Sandman] ],,ALF00866,100.0,2.30235E-47 SIF-HHPRED: Recombination Directionality Factor RdfS; Excisionase, Recombination Directionality Factor, winged helix-turn-helix, superhelix, DNA BINDING PROTEIN; HET: GOL; 2.45A {Mesorhizobium japonicum R7A},,,8DGL_A,80.5195,99.2 SIF-Syn: When checking phamerator and comparing the two most closely related phages to Sourignavong, Link and Decurro, I found that they were listed as having DNA Binding Domain Protein. This similarity in phages hints at them having synteny.
    /note=Gene 23 likely encodes a DNA-binding protein. Function prediction was based on PhagesDB, NCBI, and HHpred analyses. PhagesDB blast revealed numerous functions of phages in the same cluster (AN) as Sourignavong, with phage "arby" exhibiting a top hit E-value of 5E-37, supporting the function of a DNA binding domain protein. NCBI blast further reinforced this with a top hit E-value of 2.302E-47. Although HHPred yielded a decent E-value (0.0028), it provided comparatively less abundant evidence compared to PhagesDB blast and NCBI Blast.

CDS 14185 - 14853
  /gene="24"
  /product="gp24"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Sourignavong_24"
    /note=Original Glimmer call @bp 14185 has strength 7.3
    /note=SSC: 14185-14853 CP: yes SCS: glimmer ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Arthrobacter phage Link]],,NCBI, q1:s1 100.0% 4.71943E-160 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.904, -3.2391149694189205, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Arthrobacter phage Link]],,ASR83583,99.0991,4.71943E-160 SIF-HHPRED: CHROMOSOME REPLICATION INITIATION PROTEIN; DNAD, DNA REPLICATION, PRIMOSOME, REPLICATION; 2.3A {GEOBACILLUS KAUSTOPHILUS HTA426},,,2VN2_D,34.6847,98.4 SIF-Syn: there is synteny between gene 24 in Sourignavong, and genes 23 of Decurro and Link which are phages in the same cluster (AN).
    /note=DNA binding protein function is supported by the phages DB blast of phage (Link) w/ an E-value of 1e-109. In addition, the HHPred is supportive. NCBI Blast is supportive as well with an E-value of 3.73E-103.

CDS 14840 - 15055
  /gene="25"
  /product="gp25"
  /function="hypothetical protein"
  /locus tag="Sourignavong_25"
    /note=Original Glimmer call @bp 14840 has strength 3.45
    /note=SSC: 14840-15055 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein SEA_DECURRO_24 [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 1.48356E-45 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.405, -2.17469248771465, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DECURRO_24 [Arthrobacter phage Decurro] ],,YP_009191317,100.0,1.48356E-45 SIF-HHPRED: DUF3007 ; Protein of unknown function (DUF3007),,,PF11460.12,35.2113,75.2 SIF-Syn: 
    /note=Function unknown based on Phagesdb BLAST, HHpred, NCBI Blast.

CDS 15052 - 15345
  /gene="26"
  /product="gp26"
  /function="hypothetical protein"
  /locus tag="Sourignavong_26"
    /note=Original Glimmer call @bp 15052 has strength 6.04; Genemark calls start at 15052
    /note=SSC: 15052-15345 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_DECURRO_25 [Arthrobacter phage Decurro] ],,NCBI, q1:s1 100.0% 1.89526E-63 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.864, -3.5290106867422555, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DECURRO_25 [Arthrobacter phage Decurro] ],,YP_009191318,100.0,1.89526E-63 SIF-HHPRED: YscM2; Chaperone, type III secretion; 2.38A {Yersinia pestis},,,1TTW_B,22.6804,49.1 SIF-Syn: Gene 25 in Decurro and Link does not have a known function.
    /note=Strong support for unknown functions. E-values are low ( all less than e-1). all functions in HHRED have extremely hight E-values (all above 44). many closely related phages do not have a known function for this gene. in NCBI all E-values are lower than 1.79976e-17 for unknown functions.