TABLE 2.
Chromosomal DNA fragments present in C. jejuni 81-176 but not in C. jejuni NCTC 11168
| Function and ORF | Lengtha (bp) | % G+C content | Closest relationshipb | Identity (%)c | Accession no. |
|---|---|---|---|---|---|
| Capsule | |||||
| Cj81-045 | 1,0203′ | 26.6 | Putative glycosyltransferase, C. jejuni ATCC 43456 (AAR01891) | 334/340 (98) | AY681253 |
| Cj81-046 | 3193′ | 30.7 | Putative dTDP-4-dehydro rhamnose 3,5-epimerase C. jejuni ATCC 43456 (AAR01889) | 106/106 (100) | AY681254 |
| Cj81-047 | 5645′ | 19.1 | Putative glycosyltransferase, C. jejuni ATCC 43456 (AAR01890) | 139/177 (78) | AY681254 |
| Cj81-062 | 5943′ | 24.7 | Putative glycosyltransferase, C. jejuni ATCC 43456 (AAR01890) | 198/198 (100) | AY681260 |
| Cj81-063 | 1705′ | 30.4 | Putative glycosyltransferase, C. jejuni ATCC 43456 (AAR01891) | 44/56 (78) | AY681260 |
| Cj81-079 | 1,0583′ | 25.6 | Putative glycosyltransferase, C. jejuni CCUG 10954 (AAR01916) | 303/333 (90) | AY681267 |
| Cj81-080 | 1,0115′ | 21.9 | Putative glycosyltransferase, C. jejuni ATCC 43456 (AAR01894) | 547/603 (90) | AY681267 |
| Cj81-081 | 1,613 | 21.9 | Putative glycosyltransferase, C. jejuni ATCC 43456 (AAR01896) | 535/536 (99) | AY681267 |
| Cj81-102 | 5805′3′ | 21.6 | Putative glycosyltransferase, C. jejuni ATCC 43456 (AAR01892) | 176/192 (91) | AY681278 |
| Cj81-103 | 468 | 22.0 | Putative glycosyltransferase, C. jejuni ATCC 43456 (AAR01881) | 154/155 (99) | AY681279 |
| Cj81-128 | 5315′ | 34.0 | Putative GDP-mannoheptose-4,6 dehydratase, C. jejuni ATCC 43456 (AAR01886) | 142/143 (99) | AY681295 |
| Cj81-129 | 4585′ | 25.6 | Unknown, C. jejuni ATCC 43456 (AAR01888) | 151/151 (100) | AY681296 |
| Cj81-130 | 3843′ | 31.2 | Putative GDP-fucose synthase, C. jejuni ATCC 43456 (AAR01887) | 113/127 (88) | AY681296 |
| Lipooligosaccharide, cell envelope, and surface structures | |||||
| Cj81-003 | 1943′ | 26.3 | Putative acetyltransferase, C. jejuni ATCC 43449 (AAL06009) | 47/47 (100) | AY681239 |
| Cj81-008 | 6035′ | 22.2 | Beta-1,4-N-acetylgalactosaminyltransferase, C. jejuni OH4384 (AAF31769) | 200/200 (100) | AY681241 |
| Cj81-009 | 2805′ | 20.3 | Beta-1,3-galactosyltransferase, C. jejuni OH4384 (AAF31770) | 59/92 (64) | AY681241 |
| Cj81-010 | 3603′ | 27.1 | Beta-1,3-galactosyltransferase, C. jejuni OH4384 (AAF31770) | 120/120 (100) | AY681242 |
| Cj81-011 | 8533′ | 25.8 | Alpha-2,3-sialyltransferase, C. jejuni OH4384 (AAF34137) | 269/284 (94) | AY681242 |
| Cj81-030 | 1825′ | 25.7 | Putative amino acid-activating enzyme Cj1307, C. jejuni NCTC 11168 (NP_282453) | 48/60 (80) | AY681244 |
| Cj81-042 | 6465′3′ | 24.5 | Putative lipopolysaccharide A protein, Vibrio parahaemolyticus RIMD 2210633 (NP_796570) | 82/200 (41) | AY681251 |
| Cj81-043 | 8395′ | 24.3 | Putative glycosyltransferase, C. jejuni OH4384 (AAF31768) | 243/277 (87) | AY681252 |
| Cj81-044 | 1673′ | 19.8 | Beta-1,4-N-acetylgalactosaminyltransferase, C. jejuni OH4384 (AAF31769) | 46/50 (92) | AY681252 |
| Cj81-058 | 7783′ | 31.7 | Beta-1,4-N-acetylgalactosaminyltransferase, C. jejuni ATCC 43456 (AAL05993) | 259/259 (100) | AY681257 |
| Cj81-059 | 6535′ | 26.4 | NeuC1, C. jejuni 81-176 (AAL09370) | 215/217 (99) | AY681257 |
| Cj81-085 | 1,442 | 24.7 | Penicillin-binding protein 1A, Oceanobacillus iheyensis HTE831 (NP_692087) | 53/137 (38) | AY681270 |
| Cj81-104 | 4295′3′ | 34.0 | Probable periplasmic protein Cj0737, C. jejuni NCTC 11168 (NP_281909) | 84/131 (64) | AY681280 |
| Cj81-106 | 558 | 34.2 | Sialic acid synthase, C. jejuni ATCC 43449 (AAL06005) | 185/185 (100) | AY681282 |
| Cj81-119 | 853 | 33.0 | FlgE, C. jejuni 81-176 (AAP34261) | 284/284 (100) | AY681288 |
| Cj81-121 | 644 | 28.2 | Probable outer membrane protein Cj1721c, C. jejuni NCTC 11168 (NP_282847) | 140/214 (65) | AY681290 |
| Cj81-127 | 5403′ | 28.6 | a) Unknown, C. jejuni 81-176 (AAR82939) | 180/180 (100) | AY681294 |
| b) Putative glycosyltransferase WavM, Vibrio cholerae (AAL77351) | 67/187 (35) | ||||
| Restriction-modification, recombination, and repair (DNA modification) | |||||
| Cj81-032 | 2993′ | 31.4 | Type I site-specific restriction-modification system, Trichodesmium erythraeum IMS101 (ZP_00071585) | 31/86 (36) | AY681246 |
| Cj81-057 | 1,268 | 27.7 | Type I restriction-modification system S subunit, Synechocystis sp strain PCC 6803 (BAD02014) | 138/428 (32) | AY681256 |
| Cj81-060 | 6905′3′ | 34.0 | a) Type I site-specific restriction-modification system, Haemophilus influenzae (ZP_00321696) | 125/241 (51) | AY681258 |
| b) Type I restriction enzyme HsdR, putative Vibrio cholerae O1 biovareltor strain N16961 (NP_231400) | 122/244 (50) | ||||
| Cj81-061 | 3375′3′ | 30.6 | Putative type I restriction-modification system (HsdR), Acinetobacter sp. strain ADP1 (YP_047908) | 70/113 (61) | AY681259 |
| Cj81-087 | 4195′ | 26.4 | a) Probable type IIS restriction-modification enzyme, C-terminal half Cj0032 C. jejuni NCTC 11168 (NP_281254) | 89/141 (63) | AY681270 |
| b) Type I restriction enzyme HsdR, putative Vibrio cholerae O1 biovareltor strain N16961 (NP_231400) | 55/122 (45) | ||||
| Cj81-118 | 9413′ | 32.7 | Type I restriction-modification system methyltransferase subunit, Trichodesmium erythraeum IMS101 (ZP_00071587) | 183/318 (57) | AY681287 |
| Cj81-126 | 4485′3′ | 30.3 | a) Type I restriction-modification system specificity subunit, Methanosarcina mazei Go1 (NP_635005) | 69/128 (53) | AY681293 |
| b) Type I restriction-modification system methyltransferase subunit, Trichodesmium erythraeum IMS101 (ZP_00071587) | 183/318 (57) | ||||
| Small-molecule metabolism | |||||
| Cj81-005 | 8593′ | 34.8 | Cytochrome c family protein, Geobacter sulfurreducens PCA (NP_951335) | 128/281 (45) | AY681240 |
| Cj81-006 | 584 | 25.3 | a) Conserved hypothetical protein, Wolinella succinogenes DSMZ 1740 (NP_908252) | 66/184 (35) | AY681240 |
| b) Thiol-disulfide interchange protein HP0377, H. pylori 26695 (NP_207175) | 54/180 (30) | ||||
| Cj81-007 | 4925′ | 30.6 | Cytochrome c biogenesis protein (YCF5), Wolinella succinogenes DSMZ 1740 (NP_908253) | 70/152 (46) | AY681240 |
| Cj81-038 | 2065′ | 25.1 | Glutamate synthase (NADPH) large-chain Cj0007 precursor, C. jejuni NCTC 11168 (NP_281229) | 68/68 (100) | AY681247 |
| Cj81-041 | 7005′3′ | 26.0 | a) Hypothetical protein Cj1300, C. jejuni NCTC 11168 (NP_282446) | 126/229 (55) | AY681250 |
| b) 3-Demethylubiquinone-9 3-methyltransferase, Bacteroides thetaiotaomicron VPI-5482 (NP_811691) | 41/124 (33) | ||||
| Cj81-074 | 5133′ | 34.8 | Predicted acyl esterases, Rhodobacter sphaeroides (ZP_00007094) | 92/151 (60) | AY681266 |
| Cj81-083 | 6415′3′ | 30.9 | a) Hypothetical protein WS1432, Wolinella succinogenes DSMZ 1740 (NP_907593) | 87/211 (41) | AY681268 |
| b) Anaerobic DMSO reductase chain C, Haemophilus influenzae Rd KW20 (NP_439204) | 46/185 (24) | ||||
| Cj81-088 | 1,1675′3′ | 28.7 | Cytochrome c biogenesis protein YCF5, Wolinella succinogenes DSMZ 1740 (NP_908253) | 196/393 (49) | AY681271 |
| Cj81-095 | 1,0535′ | 30.4 | 8-Amino-7-oxononanoate synthase BioF, C. jejuni NCTC 11168 (CAB72773) | 243/350 (69) | AY681274 |
| Cj81-097 | 5793′ | 32.6 | Cytochrome c family protein, Geobacter sulfurreducens PCA (NP_951335) | 60/204 (29) | AY681275 |
| Cj81-098 | 443 | 30.2 | a) Cytochrome b subunit of formate dehydrogenase, Dechloromonas aromatica (ZP_00151826) | 59/189 (31) | AY681275 |
| b) Nitrate-TMAO reductases, membrane-bound tetraheme cytochrome c subunit, Desulfitobacterium hafniense taxon:49338 (ZP_00099300) | 48/133 (36) | ||||
| Cj81-099 | 1,1415′3′ | 35.7 | Cytochrome c, putative Shewanella oneidensis MR-1 (NP_716115) | 235/376 (62) | AY681276 |
| Cj81-105 | 1,6275′3′ | 35.1 | Anaerobic DMSO reductase chain A (DmsA), Wolinella succinogenes DSM 1740 (NP_907591) | 325/513 (63) | AY681281 |
| Cj81-109 | 8933′ | 25.1 | Acyl dehydratase, Azotobacter vinelandii (ZP_00089607) | 18/41 (43) | AY681284 |
| Cj81-110 | 227 | 23.2 | Probable acyl carrier protein Cj1299, C. jejuni NCTC 11168 (NP_282445) | 44/75 (58) | AY681284 |
| Cj81-111 | 7585′ | 28.2 | a) Hypothetical protein Cj1298, C. jejuni NCTC 11168 (NP_282444) | 110/242 (45) | AY681284 |
| b) Aminoglycoside N3′-acetyltransferase, Clostridium acetobutylicum (NP_348814) | 85/250 (34) | ||||
| Cj81-124 | 2215′ | 30.2 | Putative cytochrome c type biogenesis protein, Helicobacter pylori J99 (NP_223720) | 44/69 (63) | AY681291 |
| Transport and/or binding proteins, protein and peptide secretion | |||||
| Cj81-027 | 8223′ | 33.9 | Hypothetical protein Tgh073, C. jejuni TGH 9011 (AAS99026) | 26/26 (100) | AY681243 |
| Cj81-048 | 272 | 31.9 | a) Conserved hypothetical protein, Clostridium perfringens strain 13 (NP_561338) | 38/72 (52) | AY681255 |
| b) Putative transporter CgxT, E. coli taxon:562 (AAL61900) | 26/72 (36) | ||||
| Cj81-049 | 453 | 34.2 | Preprotein translocase chain Cj1688c, C. jejuni NCTC 11168 (NP_282814) | 116/117 (99) | AY681255 |
| Cj81-073 | 2975′ | 29.6 | a) Permeases of the major facilitator superfamily, Burkholderia cepacia R18194 (ZP_00217922) | 31/83 (37) | AY681266 |
| b) Putative transporter CgxT, E. coli taxon:562 (AAL61900) | 23/77 (29) | ||||
| Cj81-094 | 1,1033′ | 29.7 | Similar to di-tripeptide ABC transporter PLU1813, Photorhabdus luminescens subsp. laumondii (NP_929091) | 148/366 (40) | AY681273 |
| Cj81-107 | 4045′ | 29.3 | Probable efflux protein Cj1687, C. jejuni NCTC 11168 (NP_282813) | 88/129 (68) | AY681283 |
| Cj81-125 | 3515′3′ | 32.2 | Probable molybdenum transport ATP-binding protein Cj0300c, C. jejuni NCTC 11168 (NP_281491) | 77/117 (65) | AY681292 |
| Hypothetical and other | |||||
| Cj81-026 | 452 | 32.9 | a) Hypothetical protein Bucepa02004635, Burkholderia cepacia R1808 (ZP_00220764) | 60/137 (43) | AY681243 |
| b) Mating pair stabilization protein, Novosphingobium aromaticivorans (NP_049155) | 60/140 (42) | ||||
| Cj81-033 | 989 | 21.7 | Hypothetical protein, Leptospira interrogans serovar lai strain 56601 (NP_711975) | 117/309 (37) | AY681246 |
| Cj81-034 | 3265′ | 24.7 | Hypothetical protein STY3192, Salmonella enterica subsp. enterica serovar Typhi CT18 (NP_457434) | 42/58 (72) | AY681246 |
| Cj81-037 | 1,0743′ | 24.3 | Hypothetical protein jhp0174, H. pylori strain J99 (NP_222895) | 131/366 (35) | AY681247 |
| Cj81-068 | 847 | 23.5 | Hypothetical protein, Bacillus cereus ATCC 14579 (NP_831045) | 52/172 (30) | AY681264 |
| Cj81-069 | 1,319 | 24.5 | ATP/GTP-binding protein, Bacillus cereus ATCC 14579 (NP_831044) | 153/456 (33) | AY681264 |
| Cj81-070 | 4965′3′ | 24.2 | Conserved hypothetical protein, Porphyromonas gingivalis W83 (NP_905721) | 60/143 (41) | AY681265 |
| Cj81-086 | 894 | 23.8 | Hypothetical protein, Enterococcus faecalis V583 (NP_815563) | 43/140 (30) | AY681270 |
| Cj81-092 | 4203′ | 29.3 | Hypothetical protein Cj0741, C. jejuni NCTC 11168 (NP_281913) | 48/49 (97) | AY681272 |
| Cj81-096 | 611 | 27.3 | Hypothetical protein Cj0305c, C. jejuni NCTC 11168 (AL139074) | 128/203 (63) | AY681274 |
| Unknown | |||||
| Cj81-004 | 1233′ | 29.3 | No hit | AY681239 | |
| Cj81-028 | 1503′ | 30.7 | No hit | AY681244 | |
| Cj81-029 | 725 | 24.2 | No hit | AY681244 | |
| Cj81-040 | 1,1475′ | 29.4 | No hit | AY681249 | |
| Cj81-064 | 2985′ | 27.9 | No hit | AY681261 | |
| Cj81-065 | 4083′ | 31.0 | No hit | AY681261 | |
| Cj81-084 | 2755′ | 31.5 | No hit | AY681269 | |
| Cj81-093 | 1885′ | 32.8 | No hit | AY681272 | |
| Cj81-100 | 1723′ | 38.9 | No hit | AY681277 | |
| Cj81-101 | 2305′ | 37.7 | No hit | AY681277 | |
| Cj81-108 | 4465′ | 32.9 | No hit | AY681283 | |
| Cj81-115 | 3195′ | 38.0 | No hit | AY681285 | |
| Cj81-116 | 8843′ | 34.1 | No hit | AY681285 | |
| Cj81-117 | 7675′ | 26.8 | No hit | AY681286 |
a
The superscript numbers denote partial ORFs with the 3′ and/or 5′ region missing.
b
Database hits: a, first hit; b, other relevant hit.
c
Amino acid identity in the region of homology identified by BLASTP.