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Table 2 Major gene products shared among lambda-like phages induced from Mannheimia haemolytica

From: Comparative analysis of multiple inducible phages from Mannheimia haemolytica

No. (Gene name)

Size (aa)/MW (kDa)/pI

Function

Motifsa

Best homologs

% identity (aa) to Aaphi23b

Absent in phages

1 terS

174/19.1/5.4−5.6

Terminase, small subunit

Terminase_2 (pfam03592)

Bacteriophage terminase small subunit (M. haemolytica)

52−54

 

2 terL

406−410/46.3−47.3/5.9−6.1

Terminase, large subunit

Terminase_3 superfamily (cl12054)

Phage terminase, large subunit, PBSX (M. haemolytica)

19−21

 

3 porT

458−467/50.6−52.2/4.9−5.1

Portal protein

phage_prot_Gp6 (pfam05133)

Hypothetical protein (M. haemolytica)

20−25

 

4 MHP

312−553/35.4−63.3/9.3−9.5

Head morphogenesis protein

Phage_Mu_F superfamily (cl10072)

Hypothetical protein (M. haemolytica)

12−23

 

5 MTP

160/17.3/5.1

Major tail protein

Phage_tail_2 (pfam06199)

Phage major tail protein (M. haemolytica)

 

1152AP2

6

137/15.1/10.2

Hypothetical protein

DUF4128 (pfam13554)

Hypothetical protein (M. haemolytica)

 

535AP2, 3927AP1, 587AP2

7 hicB

138/15.5/4.6

HicB

UPF0150 (pfam03681)

Toxin-antitoxin , antitoxin component, HicB (M. haemolytica)

 

1152AP2

8 hicA

58/6.6/10.1

HicA

YcfA (pfam07927)

Toxin-antitoxin, toxin component, HicA (M. haemolytica)

 

1152AP2

9 TMP

816−1008/88.1−108.8/5.2−6.2

Tail length tape measure protein

Tape_meas_nterm superfamily (cl15680); TMD(1)

Tail length tape measure-related protein (M. haemolytica)

17−19

 

10 M

107−109/12.3−12.5/8.8−9

Minor tail protein M

Phage_min_tail (pfam05939)

Gifsy-1 prophage VmtM (M. haemolytica)

  

11 L

156/17.6/5

Minor tail protein L

Phage_tail_L superfamily (cl01908)

Phage-related minor tail protein L (M. haemolytica)

 

1152AP2

12 L

238/26.5/6−6.3

Minor tail protein L

Phage_tail_L superfamily (cl01908)

Phage minor tail protein L (M. haemolytica)

  

13 K

243/28.5/5.3

Minor tail protein K

MPN_NLPC_P60 (cd08073)

Bacteriophage tail protein (M. haemolytica)

  

14 I

196−209/20.9−22.1/9.6−9.9

Tail assembly protein I

Lambda_tail_I superfamily (cl01945); TM(2)

Bacteriophage tail protein and tail assembly protein I (M. haemolytica)

15−19

 

15 J

1954−2352/213.3−255/6.3−8

Host specificity protein J

Phage-tail_3 (pfam13550); TM(2)

Host specificity protein J (M. haemolytica)

  

16 int

329−351/37.9−40.8/9.7−9.9

Integrase

Phage_integrase (pfam00589); Phage_integ_N superfamily (cl07565); DNA_BRE_C superfamily (cl00213)

Integrase/recombinase (M. haemolytica)

17−24

 

17 MTase

163/19.2/8.3

Methyltransferease

Methyltransf_25 (pfam13649)

Putative bacteriophage methyltransferase (M. haemolytica)

 

3927AP1, 1152AP2, 587AP2

18

127/14.6/5.6

Hypothetical protein

flap endonuclease-1-like (cl14815)

Hypothetical protein (M. haemolytica)

 

535AP2, 587AP2

19 ant

218−233/26−26.9/7.1−7.7

Antirepressor protein Ant

P22_AR_N (pfam10547); P22_AR_C superfamily (cl11179); AntA superfamily (cl01430)

Antirepressor protein Ant (M. haemolytica, Avibacterium paragallinarum for 587AP2)

19−21

535AP2

20

71/8/9.9

Hypothetical protein

PRK11675 superfamily (cl08198)

Hypothetical protein (M. haemolytica)

 

535AP2, 587AP2

21

76/8.8/4.5

Hypothetical protein

KilA-N (pfam04383)

KilA-N domain-containing protein (M. haemolytica)

 

535AP2, 587AP2

22 HNH

168/19.4/9.6

HNH homing endonuclease

HNH_3 (pfam13392)

Putative HNH endonuclease (Lactococcus)

 

535AP2, 3927AP1, 1152AP2

23 MTase

198/21.3/8.3

Cytosine-specific DNA methyltransferease

Cyt_C5_DNA_methylase superfamily (cl18939)

Cytosine-specific methyltransferase (Haemophilus parasuis)

 

535AP2, 3927AP1, 1152AP2

24 PK

150/17.1−17.3/4.8−5

Pyruvate kinase

 

Hypothetical protein and pyruvate kinase (M. haemolytica)

  

25 exo

211−225/23.5−25.9/ 4.8−5.9

Exonuclease

YqaJ (pfam09588)

Bacteriophage exonuclease (M. haemolytica)

  

26 bet

264−307/29.2−35.3/5.2−5.3

Recombinase

RecT (pfam03837); bet_lambda (TIGR01913)

Bet protein (M. haemolytica)

  

27

154/17.9/6.5

Hypothetical protein

NTP-PPase_u3 (cl16941)

Hypothetical protein (M. haemolytica)

  

28 higB

91/10.8/6.9

HigB

HigB (COG3549)

Plasmid maintenance system killer (M. haemolytica)

 

587AP2

29 higA

101/11.4/8.1

HigA

Antidote_HigA (TIGR02607)

Plasmid maintenance system antidote protein (M. haemolytica)

 

587AP2

30 TRase

346/39.6/8.8

Transposase

HTH_28 (pfam13518)

Transposase (M. haemolytica)

 

587AP2

31 xhlA

161/18.5/5.5−5.8

Hypothetical protein

XhlA (pfam10779); TM (1)

Hypothetical protein (M. haemolytica)

  

32 cI

219−228/24.8−26.3/4.9−5.5

CI repressor

S24_LexA-like (cd06529)

LexA family repressor/S24 family protease (M. haemolytica); bacteriophage transcriptional regulator (Haemophilus parasuis, for 587AP2)

20−24

 

33 cro

68−90/7.5−10.1/6.1−9.1

Cro repressor

HTH_XRE (cd00093)

XRE family transcriptional regulator (M. haemolytica)

14−28

 

34 cII

86/9.8/8

CII protein

 

Bacteriophage CII protein (M. haemolytica)

23

587AP2

35

80/9/9.6

Hypothetical protein

HTH_39 (pfam14090)

Hypothetical protein (M. haemolytica)

 

535AP2, 3927AP1, 1152AP2

36 O

276−289/31.8−33.3/8.9−9.1

Replication protein O

Phage_rep_O (pfam04492)

Bacteriophage replication protein (M. haemolytica)

18−21

587AP2

37 P

215/24.9/9.2

Replication protein P

Phage_lambda_P superfamily (cl06169)

Putative bacteriophage replication protein (M. haemolytica)

13

535AP2, 3927AP1, 1152AP2

38 hel

453/50.9/5.7

Helicase

DnaB (TIGR00665)

Replicative DNA helicase (M. haemolytica)

 

587AP2

39 MTase

178/20.7/8.8

Methyltransferase

MT-A70 (pfam05063)

Hypothetical protein and modification methylase MunIM (M. haemolytica)

 

587AP2

40 MTase

190/21.6/5

DNA N-6-adenine-methyltransferas

Dam superfamily (cl05442)

DNA N-6-adenine methyltransferase (M. haemolytica)

 

535AP2, 3927AP1, 1152AP2

41

150−168/17.7−19.9/6.1−8.6

Hypothetical protein

DUF1367 superfamily (cl06231)

Hypothetical protein (M. haemolytica)

  

42 ninG

189/22.3/9.7

NinG protein

NinG (pfam05766)

Protein NinG (M. haemolytica)

43

587AP2

43

94/10.6/9

Hypothetical protein

DUF1364 (pfam07102)

Hypothetical protein (M. haemolytica)

 

535AP2, 3927AP1, 1152AP2

44 RusA

122/13.9/9.4

Endodeoxyribonuclease RusA

RusA (pfam05866)

Endodeoxyribonuclease RusA (Haemophilus influenzae)

 

535AP2, 3927AP1, 1152AP2

45 Q

121−157/14.3−18.6/9.2−9.5

Antitermination protein Q

Phage_antitermQ (pfam06530)

Phage anti termination protein Q (M. haemolytica)

18−22

 

46 S

81−117/9.5−12.8/9−9.3

Holin

Phage_holin_3 superfamily;TM (1–3)

Hemophilus-specific protein (M. haemolytica)

11−17

 

47 R

189−197/21.2−22.3/9.1−9.5

Endolysin

endolysin_autolysin (cd00737); lysozyme_like superfamily (cl00222); TM (1)

Lysozyme (M. haemolytica)

21−55

 

48 Rz

116/13.2/7.8−8.6

Lytic protein Rz

DUF2570 (pfam10828); TM (1)

Hypothetical protein (M. haemolytica)

34−36

 

49 Rz1

57−74/6.6−8.4/5−8

Lytic protein Rz1

 

Hypothetical protein (M. haemolytica)

30−44

 
  1. aTM: transmembrane α-helice; only 1152AP2 contains domain of Tape_meas_nterm superfamily (cl15680) and 587AP2 contains Phage_holin_3 superfamily; only protein J from 1152AP2 contains 2 TM
  2. bIdentity of amino acids sequence was calculated by ALIGN [66]