Phage P1 Summary of Genes

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P1 Gene products (listed by gene position) from Supplemental Table S1 Łobocka, MB et al. (2004) [1]

a Gene products marked by an asterisk were either purified or identified in PAGE gels.

b Coordinates of genes refer to their positions in the P1 c1-100 mod749::IS5 genome without its non-integral parts, IS5 and the associated 4-bp duplication. Coordinates of protein-coding genes are from the initial codon through the first stop codon.

c Conserved motifs of amino acid sequences were detected as described in Materials and Methods. Motif abbreviations used: HTH: helix-turn-helix, TMH: transmembrane helix, SP: signal peptide. The name of each motif is followed by its coordinates in the protein sequence. Abbreviations used to describe homologies: r.: region of amino acid residues, idt.: identical. Accession numbers or locus names of P1 protein homologs in data bases as well as their lengths in amino acid residues (aa) are given in parentheses. Amino acid sequences of P1 protein homologs marked with a superscript T can be found in the T4 and T4-like phages data base (http://phage.bioc.tulane.edu/).

d References marked by an asterisk concern identification of a protein or RNA product of a given gene; those marked by a superscript S concern previously published sequences. Superscript SD, published sequence differs internally from sequences presented here; superscript SP, published sequence is partial.


<protect>

Name {former names}a Closest homologs {amino acid sequence motifs}c Basis for name; known or proposed function Referencesd

Cra {gpORF0}{gpORF1}

r. 12-72 43% idt. to r. 9-70 of putative regulatory protein of Yersinia pestis virulence plasmid pAM1 (T15034; 71 aa)

putative cre-associated function

302S [2]

Cre*

24 % idt. to integrase-like protein of Pseudomonas sp. transposon Tn5041 (351 aa; CAA67462); similar to prokaryotic integrases and recombinases; {TMH: 163-177}

cyclization recombinase; cyclizes P1 DNA at redundant loxP sites on infection; resolves dimers, oligomers; may also modulate copy number

7*[3], 10[4], 21[5], 106[6], 182[7], 302S [2]

C8

establishment of lysogeny?

280[8], 281[9] this workS

Ref

{TMH: 95-105}

recombination enhancement function; aids microhomology recognition, maximal function requires recBCD activity

184[10], 207[11], 337[12], 338S[13]

Mat {gp1; gp18?}

particle maturation

191[14]S,346

Res* {EcoP1; R}

55% idt. to Res subunit of EcoPI of Neisseria meningitidis MC58 (NP_274282; 979 aa); similar to type III Res proteins; {DEAD-box helicase superfamily: 50-263; HTH: 749-768; TMH: 111-117}

restriction component (EcoP1) of type III restriction-modification system

68[15], 107[16]*, 145S [17], 152[18]

Mod* {M} { C2,C3}

34% idt. to Mod subunit of type III restriction-modification enzyme of Bacillus cereus (CAB40611; 669 aa); {N6_N4_Mtase DNA methyltransferase domain (pfam01555.5): 343-471}

modification and site recognition component of type III restriction-modification system; modifies pairs of 5’-AGACC sequences; host lethality of mod- alleles led to misnomers c2, c3

41[19], 42[20], 107[16]*, 145S [17], 152[18], 262 [21]

Lxc* {Bof}{C6}

lowers expression of c1, enhances binding of C1 to all its operators

164[22], 272[23], 311[24], 312, 318*S[25]

Ulx

unknown; product of gene upstream of lxc

this workS

DarB*

r. 91-274, 759-1229, 1461-1651 27%, 24%, and 25% idt. to r. 161-344, 789-1217, and 1345-1523 of putative protein of Rhizobium rhizogenes plasmid pRi1724 (NP_066674; 1693 aa); r. 49-284 27% idt. to r. 421-689 of DNA methylase-like protein of Listeria innocua (NP_569161.1, 756 aa) {SNF2 family N-terminal domain (pfam00176.5): 1046-1268; helicase conserved C-terminal domain (pfam00271.5): 1454-1517}

defence (in cis) against a subset of type I restriction enzymes e. g. EcoB, EcoK; putative DNA methyltransferase and DNA helicase; may methylate DNA during injection

155*[26],this workS

Prt {gp13, gp14?}

minor similarities to the portal protein gp20 of bacteriophage T4 (VG20_BPT4; 524 aa) and other T4-like phages; {TMH: 163-174}

portal protein (by similarity)

252[18], this workS

Pro {gp4, gp14?}

r. 34-159 30% idt. to r. 27-149 of HPr kinase of Enterococcus faecalis (HPRK_ENTFA; 310 aa); r. 115-268 22% idt. to r. 256-388 of E. coli ClpX (CLPX_ECOLI, 424 aa)

putative head processing protease; required for head morphogenesis and maturation of DarA precursor protein, homology suggests additional kinase activity

321[27], 324[28],this workS

LydE

lysis determinant, putative antiholin

this workS

LydD

{TMH: 13-32, 42-59}

lysis determinant, putative holin

this workS

Lyz {gp17}

r. 10-179 52% idt. to Yersinia pestis putative phage lysozyme (NP_405650, 170 aa); {phage lysozyme domain (pfam00959.5): 55-173}

lysozyme

277S[29]

Ssb

64% idt. to Ssb protein of S. typhi (AAF14810.1, 178 aa) {Ssb family domain (pfam00436.5): 6-114}

single stranded DNA binding protein; can complement E. coli ssb when derepressed by an lxc mutation

187S[30]

IsaA

unknown; product of IS1 associated gene

this workS

InsB

transposition protein InsB of integral P1 IS1

this workS

InsA

{HTH: 64-85}

transposition protein InsA of integral P1 IS1

this workS

IsaB

unknown; product of IS1 associated gene

149S[31]

Hxr {ORFVIII}

r. 23-80 28% idt. to r. 2-80 of Xre phage repressor of Bacillus subtilis prophage PBSX (XRE_BACSU; 113 aa) necessary for maintenance of lysogeny

homolog of xre; possible repressor protein

149S[31]

DdrB

{neutral zinc metallopeptidase zinc binding region signature (Prosite: PS00142): 869-878}

unknown; product of the second gene downstream of darA; possible protease or response regulator

149SD[31]

IddB

unknown; product of gene internal to ddrB

this work

DdrA {Vad?}

uncertain; product of the first gene downstream of darA; defect possibly causes vad (viral architecture determinant) phenotype characterized by altered P1B:P1S:P1M ratios

149S[31]

DarA* {Vad &/or Tsu?}

r. 157-279 28% idt. to r. 702-822 of Methanosarcina acetivorans chromosome segregation protein (AAM07677, 1175 aa); r. 107-293 23% idt. to r. 29-202 of Hdf

defends against restriction by type I restriction endonuclease and enables DarB to function; internal head protein processed by Pro

149S[31], 155[26]*,304*

Hdf {Gta?}

r. 29-202 23% idt. to r. 107-293 of DarA

homolog of DarA fragment; function uncertain; defect possibly causes gta (generalized transduction affected) phenotype

149S[31]

LydB {gp2}

r. 1-61 100% idt to fragment of LydB protein of p15B plasmid (Q47425, 61 aa)

lysis determinant; prevents premature lysis, LydA antagonist

149S[31],277 S[29]

LydA

100% idt. to plasmid p15B holin LydA (Q47424, 109 aa), r. 14-97 30% idt.to r. 7-89 of P1 LydC; {TMH: 7-26, 36-58}

lysis determinant; holin; promotes cell lysis

149S[31],277S[29]

LydC

r. 7-89 30% idt. to r. 14-97 of LydA holins of P1 (109 aa), and p15B plasmid (Q47424, 109 aa); {TMH: 4-23, 30-52}

lysis determinant; putative holin (by homology)

this workS

Cin*

83% idt. to DNA invertase of E. coli O157: H7 prophages VT2-Sakai (NP_308311; 184 aa) and 933H (NP_285972; 196 aa), and E. coli prophage e14 (PINE_ECOLI; 184 aa); similar to other procaryotic DNA site-specific recombinases catalysing DNA inversions; {resolvase N-terminal domain (pfam00239.5): 1-127; resolvase HTH domain (pfam02796.5): 141-182}

C-segment inversion; cix site-specific recombinase providing for alternate fiber gene expresson and hence host range enlargement; also able to fuse genomes

109[32], 135S[33],142[34], 150*[35]

gp Sv'

r. 200-518 85% idt. to variable fragment of tail fiber protein gpS of bacteriophage Mu (NP_602303, 328 aa)

variable part of the tail fiber protein (Sc+Sv'), expressed when its gene is in (-) orientation

this workS

gpU'

95% idt. to tail fiber assembly protein gpU of phage Mu (NP_602302, 177 aa); r. 73-176 21% idt. to r. 94-191 of bacteriophage λ tail fiber assembly protein Tfa

tail fiber assembly chaperone (by similarity), named after Mu homolog; variable gene of tail fiber operon, expressed when in (-) orientation; may be a virion protein

146[36],this workS

gpU* {gp20}

95% idt. to tail fiber assembly protein gpU of phage Mu (NP_050654, 175 aa); r. 51-174 30% idt. to r. 67-191 of bacteriophage λ tail fiber assembly protein Tfa

tail fiber assembly chaperone (by similarity); named after Mu homolog; expressed when in (+) orientation; may be a virion protein

142*, 146[36], this workS

gpSSc+Sv {gp19}

r. 648-985 and 175-252 85% and 39% idt., respectively to r. 162-502 and 73-150 of phage Mu tail fiber protein gpS (NP_050653, 504 aa); numerous regions of homology to tail fiber proteins of other phages {phage tail fiber repeat domain (pfam03406.4): 215-258}

tail fiber specificity, consists of a constant (Sc: aa 1-453) and variable (Sv: aa 454-987) segment; Sv is exchanged for shorter Sv' (aa 454-971) upon inversion of C-segment; named after Mu homolog

104[37], 146[36], this workS

gpR {gp11? gp12?}

98% idt. to predicted gpR of E. coli plasmid p15B (S18683, 144 aa)

tail fiber structure or assembly

104S[37]

gp16

r. 113-278 96% idt. to a fragment of tail fiber region product of E. coli plasmid p15B (ECP15BG)

baseplate or tail tube

104SP[37], 190SP[38],this workS

BplA {gp3?}

r. 9-331 24% idt. to r. 14-338 of putative protein of Desulfovibrio desulfuricans (ZP_00130636, 469 aa); r. 27-313 20% idt. to phage T4 baseplate wedge structural protein (VG6_BPT4, 660 aa)

putative baseplate structural protein (by homology), may be involved in contact between hub and wedges, as its homolog in T4

this workS

PmgA

putative morphogenetic function

this workS

Sit

r. 747-878 34% idt. to r. 131-259 of D. desulfuricans putative protein (ZP_00128659, 544 aa); r. 467-882 16% idt. to r. 1141-1545 of putative transglycosylase of B. subtilis phage SPβc2 (NP_046584.1, 2285 aa); r. 749-870 30% idt. to r. 14-138 of internal virion protein D of phage T7 (VIVD_BPT7, 1318 aa); r. 450-691 21% idt. to r. 306-548 of T4-related phage RB69 gp29 protein (NP_861896, 590 aa)

structural injection transglycosylase; putative tail tube “ruler”

190S[38]

PmgB

r. 85-120 38% idt. to r. 80-111 of T4-related RB49 bacteriophage essential base plate hub subunit protein (26_RB49T; 209 aa)

putative morphogenetic function

this workS

Tub

r. 123-180 32% idt. to r. 102-160 of tail tube protein gp19 of T4-related phage RB49 (Q9MCD9; 164 aa); r. 113-180 28% idt. to r. 92-160 of tail tube protein gp19 of T4-related phage nt-1 (Q9MCE0; 166 aa)

major tail tube protein

this workS

PmgC

r. 36-130 27% idt. to r. 75-159 of protein of unknown function of T4-like phage Aeh1 (5.1_Aeh1T; 183 aa)

putative morphogenetic function

this workS

SimC* {Sim}

{SP: 1-31}

confers superimmunity when in high copy number by blocking P1 at entry; requires removal of leader sequence

77[39], 170[40],208*S[41]

SimB {gpORF50}

{SP: 1-18}

unknown; superimmunity linked function

213SD[42],this workS

SimA

{SP: 1-17}

unknown; superimmunity linked function

C4*

antisense RNA that inhibits synthesis of Icd and Ant1/Ant2 by acting on target ant RNA; processed to its active form by RNase P

26 S[43], 33S[44],57*[45], 58[46], 112S[47], 115[48], 130S

Icd* {gpORFX}

97% idt. to putative protein x of bacteriophage P7 (PID: g628248, 73 aa)

reversible inhibition of cell division, apparently required for ant expression

123[49], 131[50], 257S*[51]

Ant1*{RebA}

r. 144-345 51% idt. to r. 67-263 of P1 KilA; r. 178-342 58% idt. to r. 74-235 of DNA-binding protein Roi of phage HK022 (NP_597902, 241 aa ), and similar to antirepressor proteins of other phages; {phage antirepressor protein domain (pfam03374.4): HTH: 256-277; coiled-coil: 219-242}

antagonism of C1 repression; forms Ant1/2-C1 complex

33S[44], 112SD[47],122[52], 131S[50], 256*[53]

Ant2*{RebB}

as above (a shorter product of ant1)

antagonism of C1 repression, forms complex with Ant1

33S[44], 112SD[47],131S[50], 256*[53]

KilA

r. 67-263 51% idt. to r. 144-345 of P1 Ant1; r. 52-259 49% idt. to r. 39-234 of phage HK022 DNA-binding protein Roi (NP_597902, 241 aa), similar to other phage antirepressor proteins

unknown, expression can kill host

112S[47], 295S[54]

RepL

{HTH: 57-78}

lytic replication, initiates replication at oriL (within repL)

112S[47], 295S[54]

RlfA

51% idt. to putative protein of Shewanella oneidensis (NP_719790, 234 aa); 53% idt. to putative protein of Haemophilus somnus (ZP_00123450, 232 aa); r. 58-185 22% idt. to r. 58-192 of putative protein of Methanobacterium thermoformicicum pFV1 plasmid (YPV2_METTF, 284 aa)

unknown; possibly replication-linked function

this workS

RlfB

33% idt. to putative protein of H. somnus (ZP_00123449, 173 aa); 40% idt. to putative protein of S. oneidensis (NP_719789, 165 aa)

unknown; possibly replication-linked function

this workS

PmgF

r. 6-66 29% idt. to r. 17-75 of putative protein of Yersinia pestis (NP_667513, 214 aa)

putative morphogenetic function

this workS

BplB

r. 23-92 25% idt. to r. 93-183 of essential base plate hub subunit of T4-related phage RB49 (26_RB49T, 209 aa)

baseplate

this workS

PmgG

putative morphogenetic function

this workS

gp21

baseplate or tail tube

323[55], this workS

gp22 {gp15?, C7?}

{phage tail sheath protein domain (pfam 04984): 234-442}

sheath protein

323[55], 325*[56], this workS

gp23 {gp15?, C7?}

r. 1-205 40% idt. to r. 1-201 of hypothetical P1-like plasmid protein of Serratia sp (AF468972.1); {TMH: 138-151}

major head protein, present in P1 heads in a full length (62 kDa) and trunkated (44 kDa) form

323[55], 325*[56], this workS

ParB*

similar to centromere binding partition proteins of ParB/SopB family of low copy number plasmids and bacteria; {HTH: 166-187}

active plasmid partitioning; binds to parS, enhances ParA-mediated repression of par operon and ATP-ase of ParA; can spread over DNA flanking parS, silencing gene expression; pairs parS loci

4SD[57], 70[58], 73[59], 83[60], 90*[61], 114[62], 203SP[63], 258[64], 343[65]

ParA*

similar to Walker-type partition ATPases of ParA/SopA family of low copy number plasmids and bacteria and to minD of E. coli and other bacteria

active plasmid partitioning; weak ATP-ase, binds to parO repressing transcription, binds to ParB-parS partition complex

4SD[57],37[66], 70[58], 73[59], 343[65]

RepA*

72% idt. to replication initiation protein of Pantoea stewartii pSW1200 plasmid (AAB66323, 278 aa); 60% idt. to replication protein of Proteus vulgaris Rts1 plasmid (REPA_ECOLI, 288 aa); {HTH: 109-130}

plasmid replication; chaperone-activated monomers initiate replication at oriR and repress own synthesis (via interaction with incC and incA); controls plasmid copy number; largely as inactive dimers

2*[67], 3[68], 6S[69]49[70], 52[71]

UpfA

46% idt. to Xenorhabdus nematophila putative prophage protein (CAB58447; 129 aa); 32% idt. to S. typhi putative prophage protein (NP_455522, 125 aa)

unknown protein function

this workS

Mlp

r. 24-90 35% idt. to r. 1-67 of LysC lysis regulator of enterobacterial phage P2 (AAM83596, 96 aa) and 29% idt. to r. 1-67 of protein of unknown function of enterobacteria phage 186 (NP_052260, 96 aa); similar to Shigella flexnerii lipoprotein Mxim precursor involved in secretion of Ipa antigens (MXIM_SHIFL, 142 aa) {prokaryotic membrane lipoprotein lipid attachment site (Prosite: PS00013): 30-40; SP: 1-46}

membrane lipoprotein precursor (by homology); possibly involved in regulation of lysis (by homology)

this workS

PpfA

{SP: 1-35}

possible periplasmic function

this workS

UpfB

unknown protein function

this workS

UpfC

r. 10-93 31% idt. to r. 10-96 of phage T4 gpORF5.4 (Y08B_BPT4, 97 aa) and 23% idt. to r. 10-92 of putative protein of Vibrio cholerae (Q9KN60; 94 aa)

unknown protein function

this workS

Uhr

unknown; product of gene upstream of hrdC

this workS

HrdC

61% idt. to E. coli nucleoid-associated putative recombination protein RdgC (RDGC_ECOLI, 303 aa); {DNA polymerase family A signature (PS00447): 117-136}

homolog of RdgC of E. coli; possibly involved in replication, recombination or/and DmtA/B function

this workS

Dmt {Dam}

r. 404-672 51% idt. to putative DNA methylase of Salmonella enterica serovar Typhi CT18 (Q8Z7Y6; 293 aa); r. 4-247 58% idt. to r. 17-238 of cytosine-specific DNA methylase of Xylella fastidiosa (Q9PCK4; 537 aa); similar to other prokaryotic N-6 adenine and C-5 cytosine specific methyltransferases

predicted bifunctional DNA methyltransferase; methylation of adenines in GATC sequences, and probably cytosines in unknown sequences (by homology); implicated in plasmid replication control, late gene expression, packaging; complements E. coli dam mutations

59[72], 66[73], this workS

tRNA1

90% idt. to predicted tRNA-Asn of Salmonella typhi plasmid pHCM2 (STYPPHCMH2)

proposed tRNA-Asn specific for the AAC codon

this workS

tRNA2

83% idt. to predicted tRNA-UGC of Synechoystis sp. (SYCSLRB)

proposed tRNA-Thr specific for the ACA codon

this workS

Plp

{prokaryotic lipoprotein attachment site (PS00013): 45-55}

unknown; putative lipoprotein

this workS

Upl

unknown; product of gene upstream of plp

this workS

TciA

41% idt. to putative TerB proteins of prophage of E. coli O157:H7 (BAB36172; 142a) and prophage CP-933R of E. coli O157:H7 EDL933 (E005369_13; 164 aa)

tellurite or colicin resistance or inhibition of cell division (by homology)

this workS

TciB

52% idt. to putative protein of cryptic prophage CP-933P of E. coli O157:H7 EDL933 (AE006460_9; 55 aa) and homologs; {SP: 1-39}

Tci accessory protein (by homology)

this workS

TciC

{TMH: 10-32}

Tci accessory protein

this workS

tRNA3

89% idt. to E. coli tRNA-Ile2, encoded by ileX (ECTRNAI)

proposed tRNA-Ile specific for the ATA codon

this workS

Ban*

78% idt. to E. coli replicative DNA helicases (DNAB_ECOLI, 471 aa) and S. typhimurium (DNAB_SALTY, 471 aa); similar to other prokaryotic replicative DNA helicases {HTH: 348-369; ATP/GTP-binding site motif A (P-loop): 217-224}

DnaB analog; complements E. coli dnaB mutants (including a null mutant); replicative DNA helicase

67, 195*S, 237, 254*

Dbn

unknown; product of gene downstream of ban

this workS

gp5

r. 3-203 22% idt. to r. 361-549 of putative Microbulbifer degradans protein (ZP_00068017, 570 aa); r. 2-180 20% idt. to r. 18-186 of putative Mesorhizobium loti protein (NP_107041; 213 aa)

baseplate

323[55], this workS

gp6 {C5?}

r. 174-333 19% idt. to r. 196-399 of gpORF194w of T4-like Aeh1 bacteriophage (Aeh1ORF194wT, 408 aa)

tail length

323[55], this workS

gp24{C5?}

baseplate or tail stability

323[55], this workS

gp7

r. 35-165 25% idt. to r. 19-154 of Shewanella. oneidensis TPR domain protein (NP_716834, 282 aa)

tail stability

323[55], this workS

gp25

r. 277-403 similar to r. 1061-1186 of non-muscle myosin II heavy chain (MYSN_ ACACA; 1509 aa) and to r. 113-230 of Pseudomonas aeruginosa TolA (TOLA_PSEAE ; 347 aa)

tail stability

323[55], this workS

gp26

r. 48-90 32% idt. to r. 36-76 of essential baseplate wedge component of T4-like Aeh1 bacteriophage (53_Aeh1T, 188 aa)

baseplate

323[55] this workS

PmgL

putative morphogenetic function

this workS

PmgM

putative morphogenetic function

this workS

PmgN

putative morphogenetic function

this workS

PmgO

r. 20-198 32% idt. to r. 15-192 of ORF7 product of P. aeruginosa phage D3 (NP_061503; 198 aa) linked to gene for D3 major capsid protein; r. 66-198 31% idt. to r. 1-128 of ORF8 product of P. aeruginosa phage D3 (NP_061504; 134 aa) following ORF7 in D3 genome

putative morphogenetic function

this workS

PmgP

putative morphogenetic function

this workS

Ppp

64% idt. to phage λ serine/threonine protein phosphatase (PP_LAMBD, 221 aa)

P1 protein phosphatase, possibly involved in head morphogenesis

this workS

PmgQ

putative morphogenetic function

this workS

PmgR {gp8?}

{TMH: 10-27}

putative morphogenetic function

this workS

PmgS {gp8?}

{coiled-coil domain: 75-220 (homologous to that of nonmuscle type myosins and SMC family proteins); HTH: 379-400}

putative morphogenetic function; possible prohead scaffolding protein

this workS

Pap

r. 12-143 25% idt. to r. 6-129 of putative protein SCO0916 of Streptomyces coelicolor (Q9RCZ4; 163 aa); r. 10-148 25% idt. to r. 156-291 of phage T4 polynucleotide kinase (PNKL_BPT4, 301 aa)

P1 acid phosphatase (by homology); possibly involved in head morphogenesis

this workS

PmgT

r. 5-239 55% idt. to r. 12-237 of S. typhi hypothetical protein (NP_569253, 243 aa), and 38% idt. to r. 4-219 of Myxococcus xantus phage Mx8 p14 protein (NP_203428, 222 aa)

putative morphogenetic function

this workS

PmgU

r. 12-55 46% idt. to r. 56-99 of ORF005c product of unknown function of T4-related phage RB49 (RB49ORF005cT; 99 aa)

putative morphogenetic function

this workS

PmgV

putative morphogenetic function

this workS

UpfM

unknown protein function

this workS

UpfN

unknown protein function

this workS

UpfO

unknown protein function

this workS

Hot

r. 5-73 61% idt. to r. 4-68 of theta subunit of E. coli DNA polymerase III (HOLE_ECOLI, 76 aa)

homolog of theta subunit of DNA polymerase III; possibly involved in phage DNA replication

this workS

Lxr

{coiled-coil domain: 157-180}

LexA regulated function

this workS

HumD*

69% idt. to UmuD homolog, gp26, of coliphage N15 (NP_046921, 128 aa); 42% idt. to processed UmuD of E. coli (BAA36030, 139 aa)

homolog of UmuD' subunit of E. coli DNA polymerase V (UmuD'UmuC); complements E. coli UmuD' defects; DNA repair

200[74], 217*[75], 276S

Phd*

100% idt. to its homolog in E. coli (CAA66837, 73 aa)

prevention of host death by Doc toxicity; confers, with Doc, addiction to P1; inactivated by ClpXP protease; represses transcription of addiction operon

95*[76], 192S[77],194[78], 210[79]

Doc*

97% idt. to its homolog in E. coli (CAA66836, 126 aa)

death on curing; toxin of P1 addiction system; reversible inhibitor of protein synthesis; corepressor of addiction operon

95[76], 121[80], 192S[77], 210[79] 211[81]*

PdcA

unknown; post-doc

192S[77], this work

PdcB {gp ORF93}

25% idt. to putative protein of E. coli (NP_ 416078, 362 aa), and E. coli O157:H7 CP-933N prophage protein (NP_287276, 349 aa), and to their homologs

unknown; post-doc

192SD[77], this work

Lpa* {gp10}

late promoter activator

111*[82], 188S[83]

PacA* {gp9}

{HTH: 19-40}

DNA packaging; cuts at pac together with PacB

286S[84], 288*[85]

PacB*

{ATP/GTP-binding site motif A(P-loop): 26-33; TMH: 68-85}

DNA packaging; cuts at pac together with PacA

286S[84], 287*[86]

C1*

99% idt. to C1 repressor of enterobacteria phage P7 (RPC1_BPP7, 283 aa); {HTH: 97-128}

controls plaque clarity; primary repressor of lytic functions

79*[87], 84[88], 124[89], 238S[90], 316[91], 319[92]

Coi* {gpORF4}

C one inactivator; forms 1:1 non-covalent complex with C1 reversibly inactivating it

25S[93], 27[94], 84S[88], 127[95],130*[96]

ImcB {gpORF3}

immunity C function; may regulate c1

27[94], 84S[88]

ImcA {gpORF2}

immunity C function; may regulate c1

27[94], 84S[88]

edit table

</protect>

a Gene products marked by an asterisk were either purified or identified in PAGE gels.

b Coordinates of genes refer to their positions in the P1 c1-100 mod749::IS5 genome without its non-integral parts, IS5 and the associated 4-bp duplication. Coordinates of protein-coding genes are from the initial codon through the first stop codon.

c Conserved motifs of amino acid sequences were detected as described in Materials and Methods. Motif abbreviations used: HTH: helix-turn-helix, TMH: transmembrane helix, SP: signal peptide. The name of each motif is followed by its coordinates in the protein sequence. Abbreviations used to describe homologies: r.: region of amino acid residues, idt.: identical. Accession numbers or locus names of P1 protein homologs in data bases as well as their lengths in amino acid residues (aa) are given in parentheses. Amino acid sequences of P1 protein homologs marked with a superscript T can be found in the T4 and T4-like phages data base (http://phage.bioc.tulane.edu/).

d References marked by an asterisk concern identification of a protein or RNA product of a given gene; those marked by a superscript S concern previously published sequences. Superscript SD, published sequence differs internally from sequences presented here; superscript SP, published sequence is partial.

References

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