TABLE 1.
C. jejuni ATCC 43431 ORFs absent from the genome of NCTC 11168a
| Category and ORF | Lengthb (bp) | %G+C content | Closest relationshipc | Accession no. | Identityd (%) | Notes | |
|---|---|---|---|---|---|---|---|
| Cell envelope and surface structures | |||||||
| Tgh001 | 774 | 23.5 | a) Unknown (C. jejuni NCTC 11828) | AAK12951 | 230/257 (89) | ||
| b) Lipooligosaccharide biosynthesis protein (Brucella melitensis) | NP_539335 | 54/207 (26) | |||||
| Tgh002 | 957 | 20.3 | a) Unknown (C. jejuni NCTC 11828) | AAK12950 | 306/318 (96) | ||
| b) Putative capsular polysaccharide synthesis protein (Bacteroides thetaiotaomicron) | NP_811784 | 88/257 (34) | |||||
| Tgh003 | 639 | 23.0 | a) Unknown (C. jejuni NCTC 11828) | AAK12949 | 196/211 (92) | ||
| b) HtrL (E. coli K-12) | NP_418075 | 60/189 (31) | |||||
| Tgh004 | 918 | 24.3 | a) Similar to C. jejuni unknown (C. jejuni NCTC 11828) | AAK12952 | 241/267 (90) | On the same contig (LOS biosynthesis locus)e | |
| b) β-1,4-N-Acetylgalactosaminyl transferase (C. jejuni O:4) | AAG43977 | 169/296 (57) | |||||
| Tgh011 | 700 | 22.4 | a) Unknown (C. jejuni NCTC 11828) | AAK12956 | 221/224 (98) | ||
| b) Glycosyltransferase (Nostoc sp. strain PCC 7120) | NP_486876 | 36/165 (21) | |||||
| Tgh020 | 357 | 23.2 | Unknown (C. jejuni NCTC 11828) | AAK12960 | 104/111 (94) | ||
| Tgh021 | 405 | 25.7 | Unknown (C. jejuni NCTC 11828) | AAK12959 | 122/134 (91) | ||
| Tgh022 | 301 | 26.2 | Putative acetyltransferase (C. jejuni NCTC 11828) | AAK12958 | 100/100 (100) | ||
| Tgh042 | 548 | 26.2 | Putative aminotransferase (C. jejuni NCTC 11828) | AAK12954 | 177/181 (97) | ||
| Tgh043 | 479 | 20.0 | a) Unknown (C. jejuni NCTC 11828) | AAK12953 | 155/159 (97) | ||
| b) Probable sugar transferase Cj1422c (C. jejuni NCTC 11168) | NP_282563 | 51/155 (32) | |||||
| Tgh101 | 462 | 26.2 | WaaV (C. jejuni NCTC 11828) | AAK12948 | 44/153 (94) | ||
| Tgh114 | 810 | 26.4 | rmlB (C. jejuni ATCC43431) | AAL06019 | 181/181 (100) | ||
| Tgh160 | 533 | 23.59 | Hypothetical protein HH0094 (Helicobacter hepaticus ATCC 51449) | AAP76691.1 | 83/162 (51) | ||
| Tgh006 | 1,7443′ | 24.6 | a) Hypothetical protein Cj1431c (C. jejuni NCTC 11168) | NP_282572 | 56/593 (92) | ||
| b) Probable sugar transferase Cj1432c (C. jejuni NCTC 11168) | NP_282573 | 36/108 (33) | On the same contig | ||||
| Tgh007 | 1305′ | 24.4 | α-2,3-Sialyltransferase (C. jejuni OH4384) | AAF13495 | 79/120 (65) | ||
| Tgh009 | 1,2443′,5′ | 24.7 | a) Unknown (Actinobacillus suis) | AAO65492 | 65/413 (39) | ||
| b) Glycosyltransferase (Nitrosomonas europaea ATCC 19718) | NP_841416 | 146/423 (34) | |||||
| Tgh010 | 6283′,5′ | 26.4 | Hypothetical membrane protein HH0255 (H. hepaticus ATCC 51449) | NP_859786 | 76/232 (32) | ||
| Tgh012 | 1,3775′ | 22.1 | a) Hypothetical protein Cj1431c (C. jejuni NCTC 11168) | NP_282572 | 112/436 (25) | ||
| b) Probable sugar transferase Cj1422c (C. jejuni NCTC 11168) | NP_282563 | 42/111 (37) | |||||
| Tgh036 | 8713′ | 20.0 | Glycosyl transferase (Nitrosomonas europaea ATCC 19718) | NP_841416 | 115/262 (43) | Linked to Tgh037 | |
| Tgh046 | 6963′ | 23.4 | Hypothetical membrane protein HH0255 (H. hepaticus ATCC 51449) | NP_859786 | 58/232 (25) | ||
| Tgh048 | 9445′ | 22.2 | Probable sugar transferase Cj1422c (C. jejuni NCTC 11168) | NP_282563 | 58/151 (38) | ||
| Tgh056 | 1,0083′,5′ | 25.8 | Hypothetical membrane protein HH0255 (H. hepaticus ATCC 51449) | NP_859786 | 90/247 (36) | ||
| Tgh059 | 1,0253′,5′ | 24.68 | Hypothetical membrane protein HH0255 (H. hepaticus ATCC 51449) | NP_859786 | 83/328 (25) | ||
| Tgh077 | 6045′ | 32.3 | a) Hypothetical protein HH0051 (H. hepaticus ATCC 51449) | NP_859582 | 79/192 (41) | ||
| b) Putative ankyrin 3-like protein (H. hepaticus) | AAL16685 | 39/82 (47) | |||||
| Tgh086 | 227 | 25.0 | Predicted periplasmic or secreted lipoprotein (Nostoc punctiforme) | ZP_00108381 | 24/78 (30) | Linked to Tgh084-88 | |
| Tgh120 | 8855′ | 25.4 | Probable sugar transferase Cj1422c (C. jejuni NCTC 11168) | NP_282563 | 183/292 (62) | ||
| Tgh126 | 2913′ | 29.2 | Probable fucose synthetase Cj1428c (C. jejuni NCTC 11168) | NP_28256 | 55/98 (56) | ||
| Tgh137 | 3043′,5′ | 28.5 | rmlA (C. jejuni ATCC43431) | AAL06018 | 100/100 (100) | ||
| Restriction-modification, recombination and repair (DNA modification) | |||||||
| Tgh014 | 4655′ | 30.3 | Type I restriction-modification system methyltransferase subunit (Trichodesmium erythraeum IMS101) | ZP_00071587 | 34/96 (35) | ||
| Tgh049 | 2,0435′ | 26.6 | a) Hypothetical protein jhp1271 (H. pylori strain J99) | NP_223990 | 312/712 (43) | ||
| b) Site-specific DNA-methyltransferase (H. pylori strain 26695) | NP_208146 | 219/481 (45) | Linked to Tgh050 | ||||
| Tgh076 | 7303′,5′ | 24.8 | a) Hypothetical protein jhp1271 (H. pylori strain J99) | G71827 | 97/197 (49) | ||
| b) Putative adenine-specific DNA methyltransferase (H. pylori 26695) | NP_208146 | 97/200 (48) | |||||
| Tgh084 | 1,3205′ | 26.9 | Putative integrase (Wolinella WS2030) | NP_908131 | 40/124 (32) | Linked to Tgh085-087 | |
| Tgh098 | 3943′,5′ | 27.9 | Putative type I specificity subunit HsdS (C. jejuni RM3200) | AAN33144 | 51/103 (49) | ||
| Tgh108 | 3245′ | 28.4 | Integrase (N. punctiforme) | ZP_00109546 | 35/99 (35) | Linked to Tgh109 | |
| Tgh117 | 5783′ | 21.9 | Integrase-recombinase protein XerCD family WS1221 (W. succinogenes DSMZ 1740) | NP_907402 | 44/119 (36) | ||
| Tgh124 | 3395′ | 25.1 | Probable type IIS restriction-modification enzyme, C-terminal half Cj0032 (C. jejuni NCTC11168) | NP_281254 | 65/101 (64) | Linked to Tgh123 | |
| Tgh128 | 3993′,5′ | 28.9 | Hypothetical protein, putative integrase WS2030 (W. succinogenes DSMZ 1740) | NP_908131 | 42/130 (32) | ||
| Tgh132 | 2833′,5′ | 28.1 | a) Conserved hypothetical protein RB1621 (Pirellula sp. strain 1) | NP_864512 | 20/65 (30) | ||
| b) ATPase involved in DNA repair (P. fluorescens PfO-1) | ZP_00085233 | ||||||
| Tgh133 | 15185′ | 22.3 | a) Conserved hypothetical protein (Rhizobium solanacearum) | NP_520740 | 87/372 (23) | ||
| b) ATPase involved in DNA repair (P. fluorescens PfO-1) | ZP_00085233 | 37/134 (27) | |||||
| Transport | |||||||
| Tgh005 | 9563′,5′ | 22.5 | Conserved hypothetical protein HH0252 (H. hepaticus ATCC 51449) | NP_859783 | 117/318 (36) | ||
| Tgh016 | 7685′ | 23.8 | a) Conserved hypothetical protein HH0252 (H. hepaticus ATCC 51449) | NP_859783 | 45/254 (57) | ||
| b) IcmF (Agrobacterium tumefaciens C58) | AH3088 | 58/206 (28) | |||||
| Tgh038 | 7383′,5′ | 24.0 | a) Conserved hypothetical protein HH0252 (H. hepaticus ATCC 51449) | NP_859783 | 101/241 (41) | ||
| b) IcmF-related protein (V. cholerae O1 biovar E Tor strain NI6961 | NP_232521 | 51/208 (24) | |||||
| Tgh051 | 6795′ | 27.8 | a) Conserved hypothetical protein HH0245 (H. hepaticus ATCC 51449) | NP_859776 | 97/227 (42) | ||
| b) ImpG involved in temperature-dependent protein secretion (R. leguminosarum bv. trifolii) | AAL17805 | 55/235 (23) | |||||
| Tgh073 | 6323′,5′ | 36.1 | TraG (N. gonorrhoeae) | AAK77139 | 46/170 (27) | ||
| Tgh103 | 9143′ | 24.2 | a) Conserved hypothetical protein HH0245 (H. hepaticus ATCC 51449) | NP_859776 | 137/301 (45) | ||
| b) ImpG (R. leguminosarum bv. trifolii) | AAL17805 | 76/303 (25) | |||||
| Tgh105 | 13065′ | 33.1 | a) Conserved hypothetical protein HH0247 (H. hepaticus ATCC 51449) | NP_859778 | 242/294 (82) | ||
| b) ImpC (R. leguminosarum bv. trifolii) | AAL17801 | 115/297 (38) | |||||
| Tgh119 | 3685′ | 27.1 | a) Conserved hypothetical protein HH0250 (H. hepaticus ATCC 51449) | NP_859781 | 62/119 (52) | ||
| b) ImpJ (R. leguminosarum bv. trifolii) | AF361470_2 | 28/108 (25) | |||||
| Chemotaxis | |||||||
| Tgh024 | 13293′ | 28.9 | Probable methyl-accepting chemotaxis signal transduction protein Cj1564 (C. jejuni NCTC 11168) | NP_282692 | 299/436 (68) | ||
| Other (bacteriophage sequence) | |||||||
| Tgh039 | 7545′ | 27.8 | Hypothetical protein y3088, possible phage protein (Yersinia pestis KIM) | NP_670387 | 36/117 (30) | ||
| Tgh088 | 401 | 23.4 | Similar to Bacillus subtilis YwlA (bacteriophage SPBc2) | NP_046626 | 19/78 (24) | Linked to Tgh089 | |
| Small-molecule metabolism | |||||||
| Tgh013 | 2823′,5′ | 17.4 | Tetrapyrrole methylases (Bacillus anthracis A2012) | NP_656000 | 16/41 (39) | ||
| Tgh017 | 8075′ | 27.5 | Hypothetical protein rodA_1 (H. pylori strain J99) | NP_223399 | 71/257 (27) | ||
| Tgh058 | 5235′ | 23.7 | a) Hypothetical protein HH0094 (H. hepaticus ATCC 51449) | AAP76691 | 84/167 (50) | ||
| b) Putative butyryltransferase (E. coli ECA95) | AAK60452 | 73/159 (45) | |||||
| Tgh106 | 9993′ | 25.2 | a) Conserved hypothetical protein HH0090 (H. hepaticus ATCC 51449) | NP_859621 | 171/327 (52) | Linked to Tgh107 | |
| b) Adenylating enzyme CmlK (Streptomyces venezuelae) | AAM01214 | 58/144 (40) | |||||
| Tgh107 | 3445′ | 31.7 | a) Conserved hypothetical protein HH0092 (H. hepaticus ATCC 51449) | NP_859623 | 102/123 (82) | Linked to Tgh106 | |
| b) Dehydrogenases (Rhodobacter sphaeroides) | ZP_00007120 | 73/109 (66) | |||||
| Hypothetical and unknown proteins | |||||||
| Tgh015 | 2513′ | 25.21 | Hypothetical protein HH0213 (H. hepaticus ATCC 51449) | NP_859744 | 31/76 (40) | ||
| Tgh018 | 18813′ | 25.7 | Hypothetical protein HH0242 (H. hepaticus ATCC 51449) | NP_859773 | 265/728 (36) | ||
| Tgh025 | 7835′ | 27.3 | Hypothetical protein HH0235 (H. hepaticus ATCC 51449) | NP_859766 | 50/155 (32) | Linked to Tgh026-028 | |
| Tgh029 | 5675′ | 22.4 | Hypothetical protein HH0253 (H. hepaticus ATCC 51449) | NP_859784 | 28/80 (35) | On the same contig | |
| Tgh030 | 993 | 31.3 | Hypothetical protein HH0254 (H. hepaticus ATCC 51449) | NP_859785 | 185/340 (54) | ||
| Tgh031 | 6773′,5′ | 28.5 | Hypothetical protein HH0383 (H. hepaticus ATCC 51449) | NP_859914 | 137/226 (60) | ||
| Tgh034 | 1965′ | 33.8 | Conserved hypothetical protein HH0243 (H. hepaticus ATCC 51449) | NP_859774 | 45/60 (75) | Linked to Tgh035 | |
| Tgh035 | 347 | 23.0 | Conserved hypothetical protein HH0251 (H. hepaticus ATCC 51449) | NP_859782 | 32/74 (43) | ||
| Tgh045 | 2273′ | 26.7 | Hypothetical protein HH1587 (H. hepaticus ATCC 51449) | NP_861118 | 43/67 (64) | Linked to Tgh044 | |
| Tgh047 | 4223′,5′ | 29.8 | Hypothetical protein HH0242 (H. hepaticus ATCC 51449) | NP_859773 | 37/88 (42) | ||
| Tgh050 | 3895′ | 28.7 | Hypothetical protein Cj0261c (C. jejuni NCTC 11168) | NP_281455 | 72/113 (63) | Linked to Tgh049 | |
| Tgh053 | 8833′,5′ | 23.1 | Hypothetical protein Cj1431c (C. jejuni NCTC 11168) | NP_282572 | 69/280 (24) | ||
| Tgh055 | 2515′ | 23.8 | Hypothetical protein (H. somnus 2336) | ZP_00132709 | 22/64 (34) | Linked to Tgh054 | |
| Tgh061 | 12743′ | 26.1 | Hypothetical protein HH0256 (H. hepaticus ATCC 51449) | NP_859787 | 149/439 (33) | ||
| Tgh071 | 464 | 24.7 | Hypothetical protein HH0212 (H. hepaticus ATCC 51449) | NP_859743 | 78/159 (49) | On the same contig and linked to Tgh070 | |
| Tgh072 | 3163′ | 27.3 | Hypothetical protein HH1374 (H. hepaticus ATCC 51449) | NP_860905 | 43/67 (64) | ||
| Tgh075 | 4913′ | 32.1 | Hypothetical protein HH0390 (H. hepaticus ATCC 51449) | NP_859921 | 57/155 (36) | ||
| Tgh079 | 11363′ | 23.9 | Hypothetical protein VCA0119 (V. cholerae O1 biovar El TOR strain N16961) | NP_232520 | 71/338 (21) | ||
| Tgh080 | 6023′ | 27.0 | Conserved hypothetical protein HH0250 (H. hepaticus ATCC 51449) | NP_859781 | 102/200 (51) | On the same contig | |
| Tgh081 | 335 | 31.2 | Conserved hypothetical protein HH0249 (H. hepaticus ATCC 51449) | NP_859780 | 46/104 (44) | ||
| Tgh082 | 4423′,5′ | 24.4 | Hypothetical protein Cj1431c (C. jejuni NCTC 11168) | NP_282572 | 37/106 (34) | ||
| Tgh083 | 5405′ | 31.1 | Hypothetical protein Chte2282 (C. thermocellum ATCC 27405) | ZP_00061855 | 25/94 (26) | ||
| Tgh085 | 449 | 25.6 | Conserved hypothetical protein HH0278 (H. hepaticus ATCC 51449) | NP_859809 | 50/108 (46) | On the same contig and linked to Tgh084 | |
| Tgh087 | 369 | 28.5 | Uncharacterized conserved protein Npun2806 (N. punctiforme) | ZP_00108380 | 33/111 (29) | ||
| Tgh089 | 305 | 30.1 | Hypothetical protein HH0264 (H. hepaticus ATCC 51449) | NP_859787 | 20/29 (68) | Linked to Tgh088 | |
| Tgh092 | 3033′ | 29.9 | Hypothetical protein HH0386 (H. hepaticus ATCC 51449) | NP_859917 | 50/102 (49) | Linked to Tgh091 | |
| Tgh093 | 287 | 27.8 | Hypothetical protein WS1132 (W. succinogenes DSMZ 1740) | NP_907321 | 47/84 (55) | Linked to Tgh095 | |
| Tgh104 | 392 | 25.7 | Conserved hypothetical protein HH0246 (H. hepaticus ATCC 51449) | NP_859777 | 43/130 (33) | ||
| Tgh115 | 196 | 30.4 | Hypothetical protein WS1734 (W. succinogenes DSMZ 1740) | NP_907859 | 25/66 (37) | Linked to Tgh116 | |
| Tgh121 | 557 | 30.1 | Hypothetical protein HH0550 (H. hepaticus ATCC 51449) | NP_860081 | 135/183 (73) | ||
| Tgh123 | 2283′ | 18.4 | Hypothetical protein ORF No. CR006 (Staphylococcus aureus MR108) | BAC67554 | 34/77 (44) | Linked to Tgh124 |
a
Only ORFs with significant protein matches in the NCBI database are reported.
a
The superscript number indicates a partial ORF with the stop codon (3′) and/or the start codon (5′) missing.
a
Only the first BLAST hit is reported if not otherwise noted as followed: a), first hit; b), second hit.
a
Identity refers to the protein identity in the region of homology identified by BLAST.
a
The complete LOS locus of ATCC 43431 was obtained by PCR and DNA sequencing of the junctions between six contigs identified by this study (Fig. 3).