This document is also available as Macintosh Microsoft WORD 5.1 and OFFICE ’98 (WORD’98) document from Sherwood Casjens.

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Table of Contents

	Introduction and Summary
Part I	Annotated Complete B31 Plasmid Gene/Pseudogene List
Part II	B31 Paralogous Gene Families
Part III	Putative B31 Plasmid Lipoprotein Genes
Part IV	The Pseudo-, Questionable, and Short Genes on the B31 Plasmids
Part V	Short Sequence Repeats in the B31 Plasmids
Part VI	Ambiguous Nucleotides in the B. burgdorferi B31 Genome Sequence
Part VII	Genome Sequence Assembly Methods
Part VIII	References

ORGANIZATION OF THIS DOCUMENT (read me first)

GENBANK ACCESSION NUMBERS and GENE NAME PREFIXES

The B. burgdorferi B31 chromosome and plasmid sequences are available at the TIGR Borrelia web site or from GENBANK. The accession numbers from GENBANK and gene name prefixes are as follows (as reported in Fraser et al. (1997) and Casjens et al. (2000):

Replicon	Accession #	gene name prefix
Chromosome	AE000788	BB0 (BBzero)
cp9	AE000791	BBC
cp26	AE000792	BBB
cp32-1	AE001575	BBP
cp32-3	AE001576	BBS
cp32-4	AE001577	BBR
cp32-6	AE001578	BBM
cp32-7	AE001579	BBO (BB"oh")
cp32-8	AE001580	BBL
cp32-9	AE001581	BBN
lp5	AE001583	BBT
lp17	AE000793	BBD
lp21	AE001582	BBU
lp25	AE000785	BBE
lp28-1	AE000794	BBF
lp28-2	AE000786	BBG
lp28-3	AE000784	BBH
lp28-4	AE000789	BBI
lp36	AE000788	BBK
lp38	AE000787	BBJ
lp54	AE000790	BBA
lp56	AE001584	BBQ

B31 Plasmid Open Reading Frame Summary

Sherwood Casjens - 1999

ALL B31 PLASMIDS

898 total gene-like entities. Among these gene-like entities are the following:

836 genes (which are not "questionable") + pseudogenes

167 pseudogenes (+ about 10 others that have marginal similarity to "intact" genes)

62 "questionable" genes (29 in-frame fragments of larger pseudogenes; 33 ²300 bp genes inside a larger pseudogene in another frame and short genes that were not called in paralogous sequence elsewhere on the plasmids).

669 "intact" genes (which are not "questionable")

39 convincing similarity hits to genes of known function outside of Borrelia among plasmid genes

16 convincing similarity hits to genes of unknown function outside of Borrelia among plasmid genes

535 "intact" genes >300 bp (which are not "questionable")

134 "intact" genes ²300 bp (which are not "questionable")

472 genes (which are not "questionable") have a paralog (it may not be intact)

197 genes (which are not "questionable") have no paralog (63 of these are >300 bp and 134 are ²300 bp)

98 plasmid gene-like entities that encode potential lipoproteins

90 intact plasmid genes that encode potential lipoproteins

7 gene-like entities that we defined as pseudogenes have translation start codons that could possibly lead to expression of lipoproteins that are truncated relative to their paralogs

32 intact plasmid genes that are below but close to our lipidation cutoff

162 paralogous gene families, 107 of which have plasmid-borne members

9 paralogous gene families encode only predicted lipoproteins

17 paralogous gene families are heterogeneous in that at least 1 potential LP and at least one non-LP is found in the family

THE "LOW PSEUDOGENE" or "WELL BEHAVED" B31 PLASMIDS

These plasmids are: cp9, cp26, all seven of the cp32s, lp28-2, lp54 and the cp32-like portion of lp56

498 gene-like entities on the "well behaved" plasmids on which apparent protein-encoding genes occupy >70% of the DNA.

9 "questionable" genes (all are ²300 bp genes inside a larger pseudogene in another frame or short genes that were not called in paralogous sequence elsewhere on the plasmids).

489 genes (which are not "questionable") + pseudogenes

22 pseudogenes

467 genes (which are not "questionable")

420 genes >300 bp (which are not "questionable")

47 genes ²300 bp (which are not "questionable")

54 genes that encode potential lipoproteins

12 genes that are below but close to our lipidation cutoff

23 convincing matches to genes of known function outside of Borrelia among plasmid genes (which are not "questionable")

13 convincing matches to genes of unknown function outside of Borrelia among plasmid genes (which are not "questionable")

THE "HIGH PSEUDOGENE" or "NOT YET AMMELIORATED" B31 PLASMIDS

These plasmids are: lp5, lp17, lp21, lp25, lp28-1, lp28-3, lp28-4, lp36, lp38, lp56 and the non-cp32-like portion of lp56

400 gene-like entities on the "bad" plasmids on which apparent protein-encoding genes occupy <75% of the DNA.

53 "questionable" genes (29 in-frame fragments of larger pseudogenes; 24 ²300 bp genes inside a larger pseudogene in another frame and short genes that were not called in paralogous sequence elsewhere on the plasmids).

347 genes (which are not "questionable") + pseudogenes

145 pseudogenes

202 genes (which are not "questionable")

115 genes >300 bp (which are not "questionable")

87 genes ²300 bp (which are not "questionable")

37 genes that encode potential lipoproteins

5 genes that are below but close to our lipidation cutoff

16 convincing matches to genes of known function outside of Borrelia among plasmid genes (which are not "questionable")

3 convincing matches to genes of unknown function outside of Borrelia among plasmid genes (which are not "questionable")

Part I

Annotated B. burgdorferi B31 Plasmid Gene List

Compiled by Sherwood Casjens, Dan Haft and Jeremy Peterson - April 1999

Definitions for Gene List

Note that these definitions are NOT necessarily absolutely identical to those used in the other published gene lists and maps for B. burgdorferi or on the TIGR WEB site. In particular we have an expanded definition of "pseudogene" that includes truncated members of paralogous gene families.

Putative genes and gene names column lists all the putative "gene-like entities" - genes and pseudogenes - currently recognized in the twenty-one B. burgdorferi B31 plasmids. We tentatively interpret those genes not indicated to be pseudogenes to be intact and potentially functional, but since the functionality of most Borrelia genes is unknown this may not be true. The gene and plasmid names used here are those used in Fraser et al. (1997) and Casjens et al. (2000). Of course any given putative pseudo-, questionable, short, fragmented or frameshifted genes could in principle have an important function, but it seems likely that a substantial fraction of them are not functional.

† Daggers mark computer-recognized ORFs that are an in-frame and part of a larger pseudogene entity. To avoid counting the entity twice, these were ignored when compiling gene and pseudogene numbers in Casjens et al. (2000).

Coordinates - these columns list the positions of the 5’ and 3’ ends of the gene or pseudogene on the sequence of the relevant plasmid.

Database hit outside Borrelia indicates all similarities to non-Borrelia sequences in the extant database as of January 1999. The criteria for inclusion in the list are those of the TIGR protocol, which uses BLAST (Altschul et al., 1997), and alignments can be found on the TIGR Borrelia WEB page. A search using EMOTIF (Nevill-Manning et al., 1998) did not find any additional convincing B31 plasmid gene similarities to previously known genes.

Common name column gives gene names previously used in the literature. If it was previously named in a strain other than B31, the Borrelia strain is given in parentheses. In addition, we and others have suggested more specific, clarifying common names for genes currently under study in the following paralogous families: mlp [family 113], bdr [80], rev [63] and erp [162/163/164] genes.

Paralog family column indicates the family of paralogous genes (homologs within B. burgdorferi B31) to which individual genes belong. A complete list of genes and pseudogenes in each of these paralogous gene families can be found in PART II of this document.

Comments Column

N-terminal lipidation consensus refers to genes whose products are most likely to be lipoproteins.

Near-consensus N-terminal lipidation signal refers to genes whose products may be lipoproteins, but whose N-terminal amino acid sequences did not quite meet the arbitrary cutoff that we set for criteria for inclusion in the "probable lipoproteins" category.

See PART III of this document for a discussion of the strategies used to identifiy possible lipoprotein encoding genes.

Authentic frameshift genes contain one or a few simple frameshifts relative to their paralogs. It is unlikely that these are actually expressed by programmed frameshifting mechanisms, since they usually do not contain the expected translationally "slippery" sequences. The TIGR computer uses this term for damaged genes (hence it currently replaces "pseudogene" in some parts of the TIGR Borrelia web page). These considered to be pseudogenes in this analysis (Casjens et al., 2000).

Authentic point mutation gene has an in-frame stop codon relative to its paralogs. These are considered to be pseudogenes in this analysis.

Gene fragments or truncated genes are substantially shorter than other members of their paralogous families. Some of these could be expressed and have a function, although they are included in the pseudogene category for ease of discussion in this analysis and to point out that they are truncated.

Pseudogenes are regions of DNA that are similar in sequence to a paralogous Borrelia gene or to a gene from another organism, but which are obviously truncated and/or do not have full open reading frames relative to those homologs. These mostly appear to be mutationally damaged genes - they include "authentic frameshift", "authentic point mutation", fused and truncated genes. These pseudogenes often contain multiple frameshifts, deletions, insertions and inversions (see Casjens et al., 2000).

Exceptions to this definition of a pseudogene are the 15 silent vlsE cassettes on lp28-1; these are not damaged are apparently "designed" to be a reservoir of antigenic variation for the vlsE protein. They are pseudogenes in that they are incomplete relative to the expressed vlsE gene and are probably not expressed themselves.

Of course the gene fragments whose reading frames are intact, that we include in this category for ease of discussion, could in fact be expressed and if so could perform a function. Nonetheless such fragments are very unusual in prokaryotes, and given the other evidence for many rearrangements in the B31 plasmids (Casjens et al., 2000) it seems likely that many, if not all of such fragments, may no longer have a biological function.

See PART IV of this document for a complete list of pseudogenes and the reasons why each is so classified.

"Questionable genes" were called by TIGR’s standard gene recognition protocol, but there is reason to suspect they may be spurious calls. For example, "computer-called genes" that are inside another gene or pseudogene and small genes that were not called in paralogous sequence elsewhere in the Borrelia sequence. Those marked with daggers (†) are inside of larger pseudogenes, but which were nonetheless called as genes by the TIGR protocol.

See PART IV of this document for a complete list of questionable genes and the reasons why each is so classified.

Short genes are <300 bp in length but ARE NOT in the "questionable" or "pseudogene" categories. The Borrelia plasmids have an inordinately large fraction of called genes that are <300 bp in length. These are often not tightly packed and fall into regions that contain no larger genes. Of course any given putative short gene could in principle be functional, but it seems likely that a substantial fraction of them are not functional

See PART IV of this document for a complete list of short plasmid "genes".

Putative functions were deduced in most cases from homologies to genes of known function.

WE EMPHASIZE ONE MORE TIME! Any given putative pseudo-, questionable, short, fragmented or frameshifted gene (as we have defined them) could in principle be functional. But it seems likely that a substantial fraction of them are not functional. We use the above pseudogene definitions only as terms to describe relevant features of the B31 plasmid genes, not to imply functionality in any specific cases.

A Complete B. burgdorferi B31 Plasmid Gene List

Putative Gene	5’end	3’end	Database hit outside Borrelia {organism of best database hit}	Common Name	Paralog Family	Comments/References
cp9						A homolog of cp9, called cp8.3 from B. garinii strain Ip21 was completely sequenced by (Dunn et al., 1994)
BBC01	163	1269			57
BBC02	1282	1836			50
BBC03	1892	2449			49
BBC04	2700	2593				short gene
BBC05	2804	3709			161
BBC06	4377	3856		eppA	95	exported protein (Champion et al., 1994)
BBC07	4788	4507				short gene
BBC08	5534	5977			55
(BBC09)						Does not exist; erroneously present in original gene list and map in figure 2 of Fraser et al. (1997)
BBC10	6808	6284			63	N-terminal lipidation consensus
BBC11	6974	7768			96
BBC12	9203	7914			165
cp26						Homolog of cp26 present in essentially all isolates (e.g., Tilly et al., 1997)
BBB01	16	321	conserved hypothetical protein {Escherichia coli}			weak similarity to acylphosphatase
BBB02	751	311
BBB03	2186	840	weak (Y-BLAST) similarity to phage N15 gene 29			The protein encoded by this gene has weak similarity to the putative "protelomerase" encoded by gene 29 of phage N15 ( Ravin et al., in preparation). Circumstantial evidence suggests this N15 protein is responsible for hairpoin end formation in the N15 prophage plasmid.
BBB04	3807	2479	PTS system, cellobiose-specific IIC component (celB) {Bacillus stearothermophilus}			possible chitobiose transporter (Fraser et al., 1997)
BBB05	4084	4428	PTS system, cellobiose-specific IIA component (celC) {Bacillus subtilis}			possible chitobiose transporter (Fraser et al., 1997)
BBB06	4440	4754	PTS system, cellobiose-specific IIB component (celA) {Bacillus subtilis}			possible chitobiose transporter (Fraser et al., 1997)
BBB07	4769	5863
BBB08	6517	5891				N-terminal lipidation consensus
BBB09	6677	7711				N-terminal lipidation consensus
BBB10	7836	8762			62
BBB11	8781	9296			50
BBB12	9275	10033	plasmid partition protein {Bacillus subtilis}		32	putative plasmid partition function
BBB13	10104	10649			49
BBB14	11417	10923				N-terminal lipidation consensus
BBB15	11636	11737				short gene
BBB16	12014	13603	oligopeptide ABC transporter, periplasmic oligopeptide-binding protein {Escherichia coli}	oppAIV	37	N-terminal lipidation consensus, not surface exposed, and not essential in culture (Bono et al., 1998)
BBB17	15107	13896	IMP dehydrogenase {Haemophilus influenzae}	guaA		IMP dehydrogenase (Margolis et al., 1994b; Zhou et al., 1997)
BBB18	16718	15135	GMP synthase {Haemophilus influenzae}	guaB		putative GMP synthase Margolis et al., 1994b) erroneous duplication in cp26 between BBB18 and BBB19 corrected in current gene list; affected originally released gene coordinates to right of BB18
BBB19	16903	17532		ospC		surface localized (Wilske et al., 1993), N-terminal lipidation consensus (Fuchs et al., 1992; Jauris-Heipke et al., 1993; Jauris-Heipke et al., 1995; Marconi et al., 1993c; Margolis et al., 1994a; Margolis et al., 1994b; Masuzawa et al., 1997; Stevenson and Barthold, 1994; Stevenson et al., 1994; Tilly et al., 1997; Wang et al., 1999; Wilske et al., 1996a; Wilske et al., 1996b); transcription start site (Marconi et al., 1993b); temperature regulation (Schwan et al., 1995; Stevenson et al., 1995)
BBB20	17733	17626				short gene
BBB21	17750	17842				short gene
BBB22	19321	17969	conserved hypothetical protein MJ0326 {Methanococcus jannaschii}		94	12 putative membrane spanning regions; homologs in E. coli
BBB23	20822	19434	conserved hypothetical protein MJ0326 {Methanococcus jannaschii}		94	12 putative membrane spanning regions; homologs in E. coli
BBB24	21364	20861				near-consensus N-terminal lipidation signal
BBB25	21851	21342				N-terminal lipidation consensus
BBB26	21898	22590
BBB27	23154	22606				N-terminal lipidation consensus
BBB28	23255	24496
BBB29	24825	26450	PTS system, maltose and glucose-specific IIABC component (malX) {Escherichia coli}		16	putative sugar transport
cp32-1
BBP01	66	1286			146
BBP02	1306	1995			147
BBP03	2011	2565			148
BBP04	2575	3336			148
BBP05	3369	3938			148
BBP06	3948	4919			149	(Casjens et al., 1997)
BBP07	4936	5394			150
BBP08	5379	5777			107
BBP09	5768	6154			108
BBP10	6154	6717			151
BBP11	6701	7810			152
BBP12	7828	8253			153
BBP13	8272	8724			154
BBP14	8724	8957			155	short gene
BBP15	8968	10239			156
BBP16	10265	10945			157
BBP17	10952	11899			159
BBP18	11920	12462			160
BBP19	12495	12824			139
BBP20	12824	13696			140
BBP21	13709	14311			141
BBP22	14324	15136			142
BBP23	15215	15415		orfA-1; blyA-1	109	putative hemolysin; short gene; sequenced for homologous plasmids in strain 297 by Porcella et al. (1996)
BBP24	15422	15766		orfB; blyB-1	111	putative hemolysin; sequenced for homologous plasmids in strain 297 by Porcella et al. (1996)
BBP25	15759	16091		orfC	112	(Gilmore and Mbow, 1998); sequenced in homologous plasmids of strain 297 by Porcella et al. (1996)
BBP26	16081	16437		orfD	143	(Gilmore and Mbow, 1998); sequenced in homologous plasmids of strain 297 by Porcella et al. (1996); near-consensus N-terminal lipidation signal but strain 297 homolog was not ipidated in E. coli.
BBP27	17060	16581		rev-1	63	N-terminal lipidation consensus (Gilmore and Mbow, 1998); sequenced in homologous plasmids of strain 297 by Porcella et al.(1996)
BBP28	17232	17675		mlpA	113	N-terminal lipidation consensus (Gilmore and Mbow, 1998); sequenced in several homologous plasmids of strain 297 by Porcella et al. (1996); lipidated in E. coli (Porcella et al., 1996); paralog lipidated in B. afzelii Theisen (1996)
BBP29	18728	17718		orf4-1	161	(Gilmore and Mbow, 1998)
BBP30	19114	20211		orf1-1	57	(Zuckert and Meyer, 1996)
BBP31	20224	20787		orf2-1	50	(Zuckert and Meyer, 1996)
BBP32	20766	21503	plasmid partition protein {Bacillus subtilis}	orfC-1	32	putative plasmid partition function (Zuckert and Meyer, 1996)
BBP33	21510	22115		orf3-1	49	(Zuckert and Meyer, 1996)
BBP34	22131	22760		bdrA	80	contains 4.7 repeats of a 54 bp sequence; all "bdr" genes contain direct, tandem repeats (Casjens et al., 1999; Zuckert and Meyer, 1996)
BBP35	23231	24553		orf8/7-1	165	(Casjens et al., 1997; Zuckert and Meyer, 1996)
BBP36	24609	25031		orf10-1	144	(Casjens et al., 1997)
BBP37	25816	25043		orf6-1	96	(Casjens et al., 1997)
BBP38	26235	26765		erpA	162	surface exposed (Lam et al., 1994); N-terminal lipidation consensus (Stevenson et al., 1996); lipidated in E. coli (Akins et al., 1995b; Wallich et al., 1995); erp-like genes have been sequenced from several other strains (Akins et al., 1999; Lam et al., 1994; Marconi et al., 1996b; Stevenson et al., 1997; Suk et al., 1995)
BBP39	26796	27929		erpB	163	N-terminal lipidation consensus (Stevenson et al., 1996)
BBP40	28074	28652			114
BBP41	28835	29398			115
BBP42	29398	30747	conserved hypothetical protein Orf26 of phage fO1205 {Streptococcus thermophilus}		145	(Amouriaux et al., 1993; Casjens et al., 1997); phage fO1205 Orf26 homology; Orf26 is a possible phage structural protein
cp32-3
BBS01	66	1286			146
BBS02	1306	1995			147
BBS03	2011	2565			148
BBS04	2575	3336			148
BBS05	3369	3938			148
BBS06	3963	4919			149	(Casjens et al., 1997)
BBS07	4936	5394			150
BBS08	5379	5777			107
BBS09	5768	6154			108
BBS10	6154	6717			151
BBS11	6701	7810			152
BBS12	7828	8253			153
BBS13	8272	8724			154
BBS14	8724	8957			155	short gene
BBS15	8968	10239			156
BBS16	10265	10945			157
BBS17	10952	11899			159
BBS18	11920	12462			160
BBS19	12495	12824			139
BBS20	12824	13696			140
BBS21	13709	14311			141
BBS22	14324	15133			142
BBS23	15212	15412		blyA-3	109	putative hemolysin; short gene
BBS24	15419	15763		blyB-3	111	putative hemolysin;
BBS25	15756	16088			112
BBS26	16078	16434			143	near-consensus N-terminal lipidation signal
BBS27	16586	16900
BBS28	16915	17046				short gene
BBS29	17068	17694		bdrF	80	contains 3.6 repeats of a 33 bp sequence
BBS30	17803	18246		mlpC	113	N-terminal lipidation consensus
BBS31	19159	18290		orf4-3	161	(Zuckert and Meyer, 1996)
BBS32	19198	19392	conserved hypothetical protein {Chlorella vulgaris}(similarity poor)			questionable gene; gene not called in paralogous sequence on other cp32s
BBS33	19605	20702		orf1-3	57	(Zuckert and Meyer, 1996)
BBS34	20715	21278			50
BBS35	21257	21994	plasmid partition protein {Bacillus subtilis}	orfC-3	32	putative plasmid partition function; (Stevenson et al., 1998b)
BBS36	22038	22577		orf3-3	49	(Stevenson et al., 1998b)
BBS37	22593	23180		bdrE	80	contains 4.1 repeats of a 54 bp sequence
BBS38	23649	25013		orf8/7-3	165	(Casjens et al., 1997)
BBS39	25069	25491		orf10-3	144	(Casjens et al., 1997)
BBS40	26276	25503		orf6-3	96	(Casjens et al., 1997)
BBS41	26708	27295		erpG; pG	164	N-terminal lipidation consensus; (Stevenson et al., 1996; Wallich et al., 1995)
BBS42	27410	27916		bapA	95	(Stevenson et al., 1996; Wallich et al., 1995)
BBS43	28067	28246				short gene
BBS44	28236	28871			115
BBS45	28871	30220	conserved hypothetical protein Orf26 of phage f01205 {Streptococcus thermophilus}		145	(Amouriaux et al., 1993; Casjens et al., 1997); phage f01205 Orf26 homology; Orf26 is a possible phage structural protein
cp32-4
BBR01	66	1286			146
BBR02	1306	1998			147	pseudogene; authentic frameshift
BBR03	2013	2573			148
BBR04	2580	3344			148
BBR05	3340	3948		orfI	148	(Casjens et al., 1997)
BBR06	3958	4929		orfII	149	(Casjens et al., 1997)
BBR07	4952	5404		orfIII	150	(Casjens et al., 1997)
BBR08	5389	5787		orfIV	107	(Casjens et al., 1997)
BBR09	5778	6164		orfV	108	(Casjens et al., 1997)
BBR10	6164	6727			151
BBR11	6711	7820			152
BBR12	7838	8263			153
BBR13	8282	8734			154
BBR14	8734	8967			155	short gene
BBR15	8978	10270			156
BBR16	10296	10889			157
BBR17	10896	11843			159
BBR18	11864	12415			160
BBR19	12448	12777			139
BBR20	12777	13649			140
BBR21	13662	14264			141
BBR22	14277	15089			142
BBR23	15167	15367		blyA-4	109	putative hemolysin; short gene
BBR24	15374	15718		blyB-4	111	putative hemolysin
BBR25	15711	16043			112
BBR26	16033	16389			143	near-consensus N-terminal lipidation signal
BBR27	16467	16994		bdrH	80	sequenced in homologous plasmids of strain 297 by Porcella et al. (1996) and in B. afzelii by Theisen (1996)
BBR28	17103	17522		mlpD	113	N-terminal lipidation consensus
BBR29	18664	17576			161
BBR30	18829	18737				questionable gene; gene not called in paralogous sequence on other cp32s
BBR31	18960	20054			57
BBR32	20067	20630			50
BBR33	20609	21361	plasmid partition protein {Bacillus subtilis}	orfC-4	32	putative plasmid partition function (Stevenson et al., 1998b)
BBR34	21415	21957		orf3-4	49	(Stevenson et al., 1998b)
BBR35	21974	22249		bdrG	80	authentic point mutation; has an in-frame stop codon
BBR36	22831	24153			165
BBR37	24210	24632		orf10-4	144	(Casjens et al., 1997)
BBR38	25435	24644		orf6-4	96	(Casjens et al., 1997); sequence from strain N40 - assession # AF011453
BBR39	25636	25538				questionable gene; gene not called in paralogous sequence on other cp32s
BBR40	25865	25966		erpH	162	pseudogene; severely truncated relative to other erps; N-terminal lipidation consensus (Stevenson et al., 1996)
BBR41	26077	26817			161/ 162	pseudogene; this is a "fusion" gene - a family [161] gene is fused to an [162] erp gene
BBR42	26853	27524		erpY	164	N-terminal lipidation consensus
BBR43	27634	28200			114
BBR44	28384	28947			115
BBR45	28947	30296	conserved hypothetical protein Orf26 of phage fO1205 {Streptococcus thermophilus}		145	homolog of phage Streptococcus thermophilus fO1205 gene orf26 that is likely to be phage structural protein; (Amouriaux et al., 1993; Casjens et al., 1997)
cp32-6
BBM01	66	1286			146
BBM02	1306	1995			147
BBM03	2010	2570			148
BBM04	2577	3341			148
BBM05	3337	3945			148
BBM06	3955	4926			149
BBM07	4949	5401			150
BBM08	5386	5784			107
BBM09	5775	6161			108
BBM10	6161	6727			151
BBM11	6711	7820			152
BBM12	7838	8263			153
BBM13	8282	8734			154
BBM14	8734	8967			155	short gene
BBM15	8978	10249			156
BBM16	10275	10955			157
BBM17	10962	11909			159
BBM18	11930	12481			160
BBM19	12514	12843			139
BBM20	12843	13715			140
BBM21	13728	14330			141
BBM22	14343	15152			142
BBM23	15231	15431		blyA-6	109	putative hemolysin; short gene
BBM24	15438	15782		blyB-6	111	putative hemolysin
BBM25	15775	16107			112
BBM26	16097	16453			143	near-consensus N-terminal lipidation signal
BBM27	17075	16596		rev-6	63	N-terminal lipidation consensus
BBM28	17247	17693		mlpF	113	N-terminal lipidation consensus
BBM29	18680	17736			161
BBM30	19069	20166			57
BBM31	20179	20742			50
BBM32	20721	21467	plasmid partition protein {Bacillus subtilis}	orfC-6	32	putative plasmid partition (Stevenson et al., 1998b)
BBM33	21520	22095		orf3-6	49	(Stevenson et al., 1998b)
BBM34	22102	22767		bdrK	80
BBM35	23241	24563			165
BBM36	24619	25041			144
BBM37	25820	25053			96	only [96] member with signal sequence
BBM38	26245	27012		erpK	164	N-terminal lipidation consensus; (Casjens et al., 1997)
BBM39	27745	27080
BBM40	27731	27850				questionable gene; gene not called in paralogous sequence on other cp32s
BBM41	27923	28486			115
BBM42	28486	29835	conserved hypothetical protein Orf26 of phage fO1205 {Streptococcus thermophilus}		145	phage fO1205 Orf26 homology; Orf26 is a possible phage structural protein; (Amouriaux et al., 1993; Casjens et al., 1997)
cp32-7
BBO01	65	1285			146
BBO02	1305	1994			147
BBO03	2010	2564			148
BBO04	2574	3335			148
BBO05	3368	3937			148
BBO06	3962	4918			149
BBO07	4935	5393			150
BBO08	5378	5776			107
BBO09	5767	6153			108
BBO10	6153	6719			151
BBO11	6703	7812			152
BBO12	7830	8255			153
BBO13	8274	8726			154
BBO14	8726	8959			155	short gene
BBO15	8970	10301			156
BBO16	10317	10955			157
BBO17	10962	11900			159
BBO18	11904	12470			160
BBO19	12503	12832			139
BBO20	12832	13707			140
BBO21	13716	14318			141
BBO22	14331	15143			142
BBO23	15222	15422		blyA-7	109	putative hemolysin; short gene
BBO24	15429	15782		blyB-7	111	putative hemolysin
BBO25	15766	16098			112
BBO26	16088	16444			143	near-consensus N-terminal lipidation signal
BBO27	16522	17136		bdrN	80
BBO28	17245	17664		mlpG	113	N-terminal lipidation consensus
BBO29	18770	17715