. 2004 Nov;186(21):7032–7068. doi: 10.1128/JB.186.21.7032-7068.2004

TABLE 3.

Gene products (listed by gene position)^a

Name^b (former name[s])	Gene coordinates^c	Coding strand	Mol mass (Da) (nucleotides in RNA)	Basis for name; known or proposed function	Reference(s)^d
Cra (gpORF0)	207-428	+	8,704	Putative cre-associated function	302^S
Cre*	436-1467	+	38,539	Cyclization recombinase acting on P1 DNA at redundant lox sites on infection; resolves dimers, etc.; possibly modulates copy no.	7,* 10, 21, 106, 182, 302^S
C8	1518-1829	+	11,313	Establishment of lysogeny?	280, 281, tw^S
Ref	2077-2637	+	21,328	Recombination enhancement function; aids microhomology recognition, maximal function requires recBCD activity	184, 207, 337, 338^S
Mat (gp1; gp18?)	2716-3468	+	28,933	Particle maturation	191, 346
Res* (EcoP1; R)	3544-6456	−	111,457	Restriction component (EcoP1) of type III restriction-modification (ResMod) system	68, 107,* 145, 152
Mod* (M, C2, C3)	6459-8399	−	73,485	Modification and site recognition component of type III ResMod system; modifies pairs of 5′-AGACC sequences	41, 42, 107,* 145,^S152, 262
Lxc* (Bof, C6)	8551-8799	−	9,645	Lowers expression of c1, enhances binding of C1 to its operators	164, 272, 311, 312, 318*^S
Ulx	8796-9236	−	17,079	Unknown; product of gene upstream of lxc	tw^S
DarB*	9270-16037	−	251,542	Defense (in cis) against a subset of type I Res enzymes, e.g. EcoB, EcoK; putative DNA methyltransferase and DNA helicase; may methylate DNA during injection	155,* tw^S
Prt (gp13, gp14?)	16113-17822	+	62,731	Portal protein (by similarity)	252, tw^S
Pro (gp4, gp14?)	17815-18834	+	36,882	Putative head processing protease and ? kinase; required for head morphogenesis and maturation of DarA precursor protein	321, 324, tw^S
LydE	18817-19029	−	7,914	Lysis determinant, putative antiholin	tw^S
LydD	18879-19133	−	9,936	Lysis determinant, putative holin	tw^S
Lyz (gp17)	19126-19683	−	20,255	Lysozyme	277^S
Ssb	19852-20340	+	18,023	Single-stranded DNA binding protein; can suppress E. coli ssb	187^S
IsaA	20370-21333	+	35,969	Unknown; product of IS1 associated gene	tw^S
InsB	21442-21945	−	19,742	Transposition protein InsB of integral P1 IS1	tw^S
InsA	21864-22139	−	9,901	Transposition protein InsA of integral P1 IS1	tw^S
IsaB	22328-22933	+	23,633	Unknown; product of IS1-associated gene	149^S
Hxr (ORFVIII)	23045-23353	−	11,033	Homolog of xre; possible repressor protein	149^S
DdrB	23343-26330	−	108,752	Unknown; product of the second gene downstream of darA; possible protease or response regulator	149^SD
IddB	25378-25776	+	13,540	Unknown; product of gene internal to ddrB	tw
DdrA (Vad?)	26343-26708	−	13,013	Uncertain; product of gene downstream of darA; defect possibly alters P1B:P1S:P1M ratios; vad (viral architecture determinant)	149^S
DarA* (Vad?, Tsu?)	26705-28624	−	69,479	Defends against restriction by type I Res endonuclease and enables DarB to function; internal head protein processed by Pro	149,^S155,* 304*
Hdf (Gta?)	28626-29228	−	22,150	Uncertain; homolog to DarA fragment; defect possibly causes gta (generalized transduction affected) phenotype	149
LydB (gp2)	29215-29658	−	17,097	Lysis determinant; prevents premature lysis, LydA antagonist	149, 277
LydA	29655-29984	−	11,433	Lysis determinant; holin; promotes cell lysis	149, 277
LydC	30052-30333	−	10,449	Lysis determinant; putative holin (by homology)	tw^S
Cin*	30461-31021	+	21,230	C-segment inversion; cix site-specific recombinase providing for alternate fiber gene expression and hence host range enlargement	109, 135, 142, 150*
gp Sv′	31016-32583	+	55,254	Variable part of S′ tail fiber; gene expressed in (−) orientation	tw^S
gpU′	32586-33119	+	20,676	Tail fiber assembly chaperone (by similarity to Mu homolog); variable gene of tail fiber operon, expressed in (−) orientation	146, tw^S
gpU* (gp20)	33148-33675	−	20,258	As gpU′, but expressed in (+) orientation; both gpU′ and gpU may be virion proteins	142,* 146, tw^S
gpS:Sc + Sv (gp19)	33679-36642	−	104,837	Tail fiber with a constant (Sc) and variable (Sv) segment as in Mu; Sv is exchanged for shorter Sv′ upon C-segment inversion	104, 146, tw^S
gpR (gp11? gp12?)	36654-37088	−	15,973	Tail fiber structure or assembly	104
gp16	37167-38003	−	31,357	Baseplate or tail tube	104,190, tw^S
BplA (gp3?)	38003-39436	−	53,577	Putative baseplate structural protein (by homology), may mediate contact between hub and wedges, as does its homolog in T4	tw^S
PmgA	39433-39789	−	13,239	Putative morphogenetic function	tw^S
Sit	39789-43211	−	120,710	Structural injection transglycosylase; putative tail tube “ruler”	190
PmgB	43293-44174	−	34,138	Putative morphogenetic function	tw^S
Tub	44189-44800	−	22,316	Major tail tube protein	tw^S
PmgC	44811-45377	−	21,017	Putative morphogenetic function	tw^S
SimC* (Sim)	45587-46399	−	30,800	Confers superimmunity when in high copy number by blocking P1 at entry; requires removal of leader sequence	77, 170, 208*^S
SimB (gpORF50)	46374-46691	−	12,033	Unknown; superimmunity-linked function	213,^SD tw^S
SimA	46713-46844	−	4,842	Unknown; superimmunity-linked function	tw^S
C4*	47144-47220	+	(77)	Antisense RNA that inhibits Icd and Ant1/Ant2 synthesis by acting on target ant RNA; processed to active form by RNase P	26, 33, 57,* 58, 112, 115, 130
Icd* (gpORFX)	47271-47492	+	8,397	Reversible inhibition of cell division, apparently required for ant expression	123, 131, 257*
Ant1* (RebA)	47489-48532	+	38,667	Antagonism of C1 repression; forms complex with Ant2	33, 112, 122, 131, 256*
Ant2* (RebB)	47738-48532	+	29,039	Antagonism of C1 repression, forms complex with Ant1	33, 112, 131, 256*
KilA	48697-49497	+	29,575	Unknown, expression can kill host	112, 295
RepL	49527-50372	+	30,857	Lytic replication, initiates replication at oriL (within repL)	112, 295
RlfA	50541-51245	+	27,716	Unknown; possibly replication-linked function	tw^S
RlfB	51245-52444	+	18,632	Unknown; possibly replication-linked function	tw^S
PmgF	51875-52171	−	11,423	Putative morphogenetic function	tw^S
BplB	52255-52764	−	18,804	Baseplate	tw^S
PmgG	52776-53357	−	20,696	Putative morphogenetic function	tw^S
gp21	53393-54208	−	29,329	Baseplate or tail tube	323, tw^S
gp22 (gp15?, C7?)	54218-55807	−	56,935	Sheath protein	323, 325,* tw^S
gp23 (gp15?, C7?)	55868-57574	−	62,248	Major head protein, present in P1 heads in full-length (62 kDa) and truncated (44 kDa) forms	323, 325,* tw^S
ParB*	57800-58801	−	37,440	Plasmid partitioning; binds to parS, enhances ParA-mediated repression of par operon and ATPase of ParA; can spread over DNA flanking parS, silencing gene expression; pairs parS loci	4, 70, 73, 83, 90,* 114, 203, 258, 343
ParA*	58818-60014	−	44,269	Plasmid partitioning; weak ATPase, binds to parO repressing transcription, binds to ParB-parS partition complex	4, 37, 70, 73,* 343
RepA*	60572-61432	−	32,219	Plasmid replication initiated by chaperone-activated monomers at oriR; represses own synthesis; binds at iterated sites (incC and incA) and can handcuff them, controling plasmid copy number	2,* 3, 6, 49, 52
UpfA	61751-62143	−	14,747	Unknown protein function	tw^S
Mlp	62155-62487	−	12,597	Membrane lipoprotein precursor (by homology); ? lysis control	tw^S
PpfA	62321-62770	−	15,744	Possible periplasmic function	tw^S
UpfB	62783-63628	−	29,310	Unknown protein function	tw^S
UpfC	63580-63864	−	9,478	Unknown protein function	tw^S
Uhr	64034-64318	+	10,781	Unknown; product of gene upstream of hrdC	tw^S
HrdC	64311-65216	+	33,638	Homolog of RdgC of E. coli; possibly involved in replication, recombination, and/or Dmt function	tw^S
Dmt (Dam)	65216-67477	+	83,595	Predicted bifunctional DNA methyltransferase; methylates A's in GATC sequences, and (by homology) probably C's at unknown sites; affects replication control, late gene expression, packaging	59, 66, tw^S
tRNA1	68149-68224	+	(76)	Proposed tRNA-Asn specific for the AAC codon	tw^S
tRNA2	68227-68302	+	(76)	Proposed tRNA-Thr specific for the ACA codon	tw^S
Plp	68273-68650	−	13,800	Unknown; putative lipoprotein	tw^S
Upl	68651-68842	−	7,092	Unknown; product of gene upstream of plp	tw^S
TciA	69034-69459	+	15,187	Tellurite or colicin resistance or inhibition of cell division (by homology)	tw^S
TciB	69459-69623	+	5,752	Tci accessory protein (by homology)	tw^S
TciC	69623-69730	+	3,719	Tci accessory protein	tw^S
tRNA3	69734-69809	+	(76)	Proposed tRNA-Ile specific for ATA codon	tw^S
Ban*	70096-71460	+	50,479	DnaB (of E. coli) analog and homolog; replicative DNA helicase	67, 195^S237, 254
Dbn	71460-72458	+	37,379	Unknown; product of gene downstream of ban	tw^S
gp5	72505-73137	−	21,669	Baseplate	323, tw^S
gp6 (C5?)	73130-74146	−	37,222	Tail length determination	323, tw^S
gp24 (C5?)	74148-74933	−	28,880	Baseplate or tail stability	323, tw^S
gp7	74920-75648	−	27,145	Tail stability	323, tw^S
gp25	75652-76869	−	45,834	Tail stability	323, tw^S
gp26	76879-77256	−	14,456	Baseplate	323, tw^S
PmgL	77436-77648	+	9,258	Putative morphogenetic function	tw^S
PmgM	77651-78229	+	21,888	Putative morphogenetic function	tw^S
PmgN	78296-78451	+	5,593	Putative morphogenetic function	tw^S
PmgO	78393-79055	+	24,217	Putative morphogenetic function	tw^S
PmgP	78953-79579	+	23,198	Putative morphogenetic function	tw^S
Ppp	79579-80253	+	25,568	P1 protein phosphatase, possible role in head morphogenesis	tw^S
PmgQ	80250-80951	+	26,912	Putative morphogenetic function	tw^S
PmgR (gp8?)	81033-81251	+	8,318	Putative morphogenetic function	tw^S
PmgS (gp8?)	81253-82515	+	48,345	Putative morphogenetic function; ? prohead scaffolding protein	tw^S
Pap	82588-83094	+	19,200	P1 acid phosphatase (by homology); ? head morphogenesis	tw^S
PmgT	83289-84218	+	35,155	Putative morphogenetic function	tw^S
PmgU	84023-84358	+	12,163	Putative morphogenetic function	tw^S
PmgV	84355-84717	+	13,975	Putative morphogenetic function	tw^S
UpfM	84900-85013	+	4,343	Unknown protein function	tw^S
UpfN	85029-85226	+	7,153	Unknown protein function	tw^S
UpfO	85204-85344	+	5,238	Unknown protein function	tw^S
Hot	85368-85631	+	9,694	Homolog of theta subunit of DNA polymerase III; ? replication	tw^S
Lxr	85638-86210	−	22,042	LexA-regulated function	tw^S
HumD*	86385-86774	+	14,313	Homolog of UmuD′ subunit of E. coli repair protein DNA polymerase V (UmuD′-UmuC); complements mutant UmuD′	200, 217,* 276^S
Phd*	86847-87068	+	8,132	Prevention of host death by Doc toxicity; confers, with Doc, addiction to P1; represses transcription of addiction operon	95,* 192,^S194, 210
Doc*	87068-87448	+	13,587	Death on curing; toxin of P1 addiction system; reversible inhibitor of protein synthesis; corepressor of addiction operon	95, 121, 192, 210, 211*
PdcA	87432-87632	+	7,630	Unknown; post-doc	192,^S tw
PdcB (gpORF93)	87660-88703	+	39,877	Unknown; post-doc	192, tw
Lpa* (gp10)	88792-89244	+	18,117	Late promoter activator	111,* 188^S
PacA* (gp9)	89330-90523	+	45,246	DNA packaging; cuts at pac together with PacB	286,^S 288*
PacB*	90523-92007	+	55,604	DNA packaging; cuts at pac together with PacA	286,^S 287*
C1*	92032-92883	−	32,544	Controls plaque clarity; primary repressor of lytic functions	79,* 84, 124, 238,^S316, 319
Coi* (gpORF4)	92994-93203	−	7,741	C one (reversible) inactivator; forms 1:1 complex with C1	25, 27, 84, 127, 130*
ImcB (gpORF3)	93169-93264	−	3,659	Immunity C function; may regulate c1	27, 84
ImcA (gpORF2)	93283-93396	−	4,340	Immunity C function; may regulate c1	27, 84

A more complete table, which includes pI, number of amino acid residues (or nucleotides in RNA), and features of the amino acid sequence (closest homologs and amino acid sequence motifs) is to be found as Table S1 in the supplemental material.

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

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

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; tw, this work.