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From:
Published online 2012 July 17. doi: 10.1371/journal.pone.0040683

Table 1

Open Reading Frames in the genomes of SpaA1 and BceA1.
Best matches to the closely related prophages
ORFStrandStartStopAmino AcidsB. thuringiensis israelensis ATCC 35646B. thuringiensis kurstak str. T03a001B. thuringiensis monterrey BGSC 4AJ1B. cereus AH676Comments on poorly characterized proteinsAnnotation
Structural Module (MZTP02-related)
1+8337107ZP_04117829.1ZP_04109629.1Present in many prophages and phages only of Bacillus speciesConserved phage protein
2+32453668ZP_00742394.1ZP_04117831.1ZP_04109627.1Present in many prophages and phages only of Bacillus speciesConserved phage protein
3+6871601302ZP_04109626.1Phage terminase, small subunit
4+15912865422ZP_04109625.1Phage terminase, large subunit
5+28784311475ZP_04109624.1Phage portal protein, SPP1
6+42355152303ZP_04109623.1Phage minor head protein
7+5152542488ZP_04109622.1Homolog of gp34.65 of Bacillus phage SPO1, DUF2829 family protein, present in a wide range of bacteria, phages and prophagesConserved phage protein, gp64 family
8+55046184224ZP_04109620.1Belongs to DUF4355 family; present in a wide range of bacteria, phages and prophagesPhage scaffold protein
9+62027044278ZP_04109619.1Capsid protein of gp6 family (gp6 proteins of Mycobacterial phages, eg. Mycobacterium phage Che8)Phage capsid protein gp6
10+70957403100ZP_04109617.1Head-tail connector protein, homolog of gp15 of Bacteriophage SPP1Head-tail connector protein, gp15 family
11+74007744112ZP_04109616.1Phage head-tail adaptor protein
12+77198126133ZP_04109615.1Phage portal protein, HK97 family
13+81328494118ZP_04109614.1Present mostly in prophages and phages of Firmicutes; homolog of gp11 of Bacillus phage TP21-LPhage structural protein
14+85099102195ZP_04109613.1Present in a wide range of phages and prophagesConserved phage protein
15+91499577140ZP_04109612.1Present in many phages and prophages, mostly of FirmicutesConserved phage protein
16+9613988889ZP_04109611.1Present in prophage regions of several Bacillus speciesConserved phage protein
17+988912828977ZP_04109610.1Phage tail tape measure
18+1284114319490ZP_04117974.1ZP_04109609.1Phage tail fiber protein
19+14316190251567ZP_00741743.1ZP_04117933.1ZP_04112413.1Phage minor structural protein
Replication module
20+1912520084319ZP_04113280.1Phage integrase
21+200982037993ZP_04113281.1Conserved in a wide range of bacteria, phages and prophages; DUF4055 family protein; has a coiled-coil domainUncharacterized secreted or membrane protein
22+203822059470ZP_04113282.1Holin, phage phi LC3 holin homolog
23+2059421412272ZP_04113283.1ZP_04108738.1N-acetylmuramoyl-L-alanine amidase
24-2145321782109ZP_04113284.1Conserved in a wide range of bacteria, phages and prophages; DUF2614 familyMembrane protein, contains Zn-finger
25-218512207273ZP_04113285.1XRE family transcriptional regulator
26+2253522855106ZP_04113286.1ZP_04108441.1Present in prophages and a few other genomic regions of several Bacillus speciesPhage membrane protein
27+2286624032388ZP_04113287.1ZP_04108442.1Cell division protein FtsK/SpoIIIE
28+2402224630202ZP_04113288.1ZP_04108443.1DNA-binding protein containing HTH domain
29-2463525516293ZP_00743542.1ZP_04113289.1DNA replication protein, HTH and DnaB-like domains
30-2589026990366ZP_00741791.1ZP_04114556.1DNA integration/recombination/inversion protein
31+2750828746412ZP_04118234.1DNA-binding protein containing XRE family HTH domain
32+289872911843ZP_04118233.1Present in several prophage regions of Bacillus speciesConserved phage protein
33-2914629490114ZP_04118232.1ZP_04111960.1XRE family transcriptional regulator
34+296392987578ZP_04118231.1ZP_04111959.1XRE family transcriptional regulator
35+299083009662ZP_04118230.1Transcriptional regulator, pbsX
36+301213027663ZP_04118115.1ZP_04123682.1Conserved in a wide range of bacteria, phages and prophages of FirmicutesConserved phage protein
37+303223110164ZP_04111906.1ZP_04195192.1Antirepressor
38+311263124265ZP_04117906.1Found in several prophage regions of Bacillus speciesPhage membrane or secreted protein
39+3126331577112ZP_04117905.1Conserved in a wide range of phages (including several unclassified dsDNA phages) and prophages of FirmicutesConserved phage protein
40+3185232499215ZP_04117909.1Sigma70, RNA polymerase sigma factor
41+3272333739338ZP_04117943.1ZP_04112661.1DnaD-like replication protein
42+3370234514270ZP_04117944.1ZP_04112587.1Predicted DNAreplication ATPase related to DnaC
43+345563482288ZP_04117945.1Present in several prophage regions of Bacillus species and found in Bacillus phage IEBHConserved phage protein
44+348943505854ZP_04117946.1Conserved in a wide range of bacteria, phages and prophages of Firmicutes; DUF3954 familyConserved phage protein
45+350763529171ZP_00742082.1XRE family transcriptional regulator
46-352883558799ZP_00742083.1ZP_04117947.1wHTH containing DNA binding protein, YjcQ family
Additional Regulatory and Recombination Module
47 SpaA1+357373599184ZP_04117960.1Present in prophage regions of a few Bacillus species, distantly related to Gp40 protein of Clostridium phage phi3626Conserved phage protein
47 BceA13573836208156ZP_04112932.1Present in prophage regions of a few Bacillus speciesConserved phage protein
48+3659736959120ZP_04117741.1Present in phages prophage regions of several Bacillus speciesConserved phage protein
49+369933716958ZP_04109637.1Found in phages and prophage regions of Firmicutes, several homologs in Streptococcus and Staphylococcus, including PH10_gp22 of Streptococcus phage PH10Conserved phage protein
50+372053740265No detectable homologsHypothetical protein
51+373993767792Conserved in a wide range of bacteria, phages and prophages of Firmicutes;Conserved phage protein
52+3779738183128Conserved in a wide range of bacteria, phages and prophages mostly of gram-positive organisms; Structure available (PDB:2OX7)Conserved phage protein, YopX superfamily
53+3821438744176ZP_04194915.1Recombination protein U
54+3876439081105ZP_04194916.1Present in a wide range of prophage regions of Firmicutes species; often as separately encoded Zn-finger and HTH domainsZn-finger and HTH domain containing protein
55+3910839446110ZP_04194917.1Sigma70, RNA polymerase sigma factor, positive control factor Xpf
56+394463973094ZP_04194917.1Sigma70, RNA polymerase sigma factor, positive control factor Xpf
57+403174049358No detectable homologsHypothetical protein
58+406234086580ZP_04194920.1One homolog present in the prophage region of Bacillus cereus AH676Hypothetical protein
59+408584112488ZP_04117814.1ZP_04194921.1Found in many prophages and phages only of Bacillus speciesConserved phage protein
60+412634150580ZP_00741808.1Homolog of gp34.65 of Bacillus phage SPO1, DUF2829 family protein, found in a wide range of bacteria, phages and prophagesConserved phage protein
61+415054176887ZP_00741808.1Homolog of gp34.65 of Bacillus phage SPO1, DUF2829 family protein, found in a wide range of bacteria, phages and prophagesConserved phage protein
62+4202842348106ZP_04112467.1ZP_04194922.1Present in prophage regions of several Bacillus speciesConserved phage protein
63+4237642759127|No detectable homologsHypothetical protein
The nucleotide start and stop codon positions for the SpaA1 ORFs are indicated; for the alternative ORF47, gene coordinates of BceA1 also are provided. Best matches are shown for four Bacillus genomes that contain most similar prophage regions. DUF, Domain of Unknown Function family in the PFAM database.