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Genes 2017, 8, 40; doi:10.3390/genes8010040
S1 of S3
Supplementary Materials: Genome Analysis of a
Novel Broad Host Range Proteobacteria Phage
Isolated from a Bioreactor Treating Industrial
Wastewater
Marina de Leeuw, Maayan Baron, Asher Brenner and Ariel Kushmaro
Figure S1. A phylogenetic tree of the bacteria, numbered H1–H18, tested in this work. The five
bacterial strains that were found sensitive to Aquamicrobium phage P14 are highlighted in blue. The
16S rRNA sequences of the different bacterial strains were aligned by Clustal Omega [33,34] using the
default settings. The best model for phylogenetic tree construction, TrN + G, was selected by
jmodeltest 2.1.10 [35]. It was ranked as the best model by the Bayesian information criterion (BIC) and
ranked 5th by the Akaike information criterion (AIC). Finally, the tree was constructed using MEGA6
[36] with 500 bootstrap replications.
Genes 2017, 8, 40; doi:10.3390/genes8010040
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Table S1. Open reading frames on the genome of the Aquamicrobium phage P14 and their domain matches found using blastx [29]. Only domain matches with Evalues smaller than 0.0001 are listed.
ORF
ORF1
Start
40092
End
149
Strand
+
Protein Length
202
ORF5
ORF9
ORF20
2232
3559
8101
2795
4107
8727
+
+
+
187
182
208
ORF21
8697
10010
+
437
ORF23
10677
13109
+
810
ORF24
ORF25
13106
13984
13984
14958
+
+
292
324
ORF28
15552
16331
+
259
ORF31
17015
17860
+
281
ORF32
17869
20283
+
804
Domain Hits
phage lysozyme
RrrD Phage-related lysozyme (muramidase), GH24 family
endolysin autolysin
PHA01782 superfamily
PHA00451 protein kinase
TOPRIM_primases
putative DnaG-like primase
DnaG DNA primase
DNA primase
AAA domain
DnaB helicase C terminal domain
DnaB Replicative DNA helicase
phage replicative helicase, DnaB family, HK022 subfamily
replicative DNA helicase; Provisional
DNA polymerase family A
DNA polymerase A Aquificae like
DNA polymerase A domain
DNA polymerase I–3′–5′ exonuclease and polymerase domains
DNA polymerase I
bifunctional 3′–5′ exonuclease/DNA polymerase; Provisional
hypothetical protein
5′–3′ exonuclease, C-terminal SAM fold
H3TH domain of the 5′–3′ exonuclease H3TH_53EXO
Taq DNA polymerase I and homologs
DNA polymerase I; Provisional
5′–3′ exonuclease
DNA polymerase I
RNase H superfamily
EXOIII exonuclease domain
InsA transposase
adenylation domain
DNA ligase OB-like domain
ATP dependent DNA ligase domain
oligonucleotide/oligosaccharide binding (OB)-fold domain
DNA ligase; Provisional
DNA ligase D, ligase domain
DNA-dependent RNA polymerase
DNA-directed RNA polymerase N-terminal
E-Value
2.96 × 10-14
6.81 × 10-42
1.36 × 10-40
3.17 × 10-49
2.13 × 10-10
1.18 × 10-07
5.33 × 10-09
1.91 × 10-08
1.59 × 10-05
5.66 × 10-07
2.76 × 10-06
2.29 × 10-13
4.48 × 10-08
5.24 × 10-06
1.35 × 10-30
2.76 × 10-25
1.31 × 10-21
1.79 × 10-29
4.53 × 10-28
1.50 × 10-27
3.05 × 10-41
1.47 × 10-05
Interval
52-143
22–165
22–159
22–181
54–182
109-178
89–195
40–196
39–187
154–352
171–375
118–389
93–389
125–389
386–762
378–771
480–730
386–774
388–770
459–769
13–288
198–239
Accession
pfam00959
COG3772
cd00737
PHA01782
PHA00451
cd01029
PHA02031
COG0358
TIGR01391
pfam1348
cd00984
COG0305
TIGR03600
PRK07004
pfam00476
cd08639
smart00482
COG0749
TIGR00593
PRK14975
PHA02030
pfam01367
4.13 × 10-05
198–235
cd09898
9.35 × 10-06
1.18 × 10-05
2.28 × 10-05
3.56 × 10-09
6.83 × 10-05
5.22 × 10-05
1.77 × 10-10
1.22 × 10-07
1.77 × 10-07
3.06 × 10-07
1.41 × 10-11
9.36 × 10-06
1.48 × 10-132
1.93 × 10-05
132–239
132–239
84–236
8–186
72–137
198–238
21–195
222–273
33–195
221–273
21–276
85–276
420–803
4–285
PRK05755
smart0047
TIGR00593
pfam13482
smart00479
COG3677
cd06846
pfam14743
pfam01068
cd08041
PHA02587
TIGR02779
pfam00940
pfam14700
Genes 2017, 8, 40; doi:10.3390/genes8010040
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ORF35
ORF37
ORF38
21404
23820
24897
22930
24815
25502
+
+
+
508
331
201
ORF42
31250
35209
+
1319
ORF43
ORF44
35267
37195
37195
37605
+
+
642
136
mitochondrial DNA-directed RNA polymerase
bacteriophage head to tail connecting protein
capsid protein
tail tubular protein A
lytic transglycosylase (LT) and goose egg white lysozyme
(GEWL) domain.
putative internal virion protein; provisional
transglycosylase SLT domain
internal virion protein D
phage T7 tail fiber protein
phage tail assembly chaperone protein
1.16 × 10-127
1.29 × 10-51
4.53 × 10-18
9.16 × 10-40
4–804
13–468
25–328
4–181
COG5108
pfam12236
PHA02004
PHA00428
1.05 × 10-13
27–127
cd00254
3.07 × 10-12
4.13 × 10-05
1.91 × 10-11
1.28 × 10-11
1.15 × 10-15
723–1245
32–109
7-1292
6–135
71–133
PHA03415
pfam01464
PHA00368
pfam03906
pfam16778