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. 2002 Sep;184(18):5158–5169. doi: 10.1128/JB.184.18.5158-5169.2002

TABLE 1.

Homology between ORFs in R391 and corresponding representative prokaryotic protein sequences

ORFa ORF product size (amino acids) ORF location (start, stop)b ORF product exhibits homology to: Source Identityc
Accession no.
No. Name % Amino acids
1 107 442, 119 ABC transporter permease protein Lactococcus lactis 27 25/92 NP 267026
2 106 790, 1110 Y4dL; hypothetical 21.8-kDa protein Rhizobium sp. strain NGR234 50 44/87 NP 443821
3 404 1103, 2317 Y4dM; putative protein Rhizobium sp. strain NGR234 55 224/405 NP 443822
4 66 2528, 2728 Possible DNA-binding protein Mycobacterium leprae 34 17/50 np 302574
5 int 413 3986, 2745 Integrase SXT element; Vibrio cholerae 99 410/413 AAC72397
6 89 4257, 3988 Soluble lytic murein transglycosylase Brucella melitensis 28 20/71 np 540005
7 324 5234, 4260 StbA; putative plasmid partitioning protein Plasmid R27; Salmonella enterica serovar Typhi 24 62/252 Q9RGU9
10 rumB 435 7460, 6153 SamB; UV protection protein S. enterica serovar Typhi CT18 61 256/419 np 458681
11 rumA 149 7878, 7429 RumA SXT element; Vibrio cholerae 98 147/149 AAK64594
13 302 8518, 9426 DNA polymerase III (epsilon subunit) Agrobacterium tumefaciens strain C58 39 117/300 AAL43906
14 104 9500, 9814 Polynucleotide phosphorylase Deinococcus radiodurans 33 18/53 np 295786
15 308 9883, 10809 NMA1157; hypothetical protein Neisseria meningitidis 35 93/261 np 283925
16 tnpIS15 238 11635, 10919 P22 protein IS15; Escherichia coli 100 234/234 Q56369
17 279 11096, 11935 P11 protein IS15; Escherichia coli 100 197/197 Q56370
18 202 12560, 11952 P11 protein IS15; Escherichia coli 100 197/197 Q56370
19 tnpIS15 238 12021, 12737 P22 protein IS15; Escherichia coli 100 234/234 Q56369
20 aph 271 12877, 13692 Aminoglycoside phosphotransferase Klebsiella pneumoniae 100 271/271 S16630
21 tnpIS15 238 14588, 13872 P22 protein IS15; Escherichia coli 100 234/234 Q56369
22 199 14049, 14648 P11 protein IS15; Escherichia coli 100 197/197 Q56370
23 210 14567, 15199 Putative inner membrane protein S. enterica serovar Typhimurium LT2 41 76/182 NP 463357
24 194 15196, 15780 Putative cytoplasmic protein S. enterica serovar Typhimurium LT2 61 116/188 NP 463356
25 947 15799, 18642 Putative ATPase involved in DNA repair S. enterica serovar Typhimurium LT2 62 585/943 NP 463355
26 317 18524, 19477 Putative ATPase involved in DNA repair S. enterica serovar Typhimurium LT2 43 123/280 NP 463355
27 171 19634, 20149 Putative type II restriction enzyme, methylase subunit S. enterica serovar Typhimurium LT2 56 96/171 NP 463354
28 tnp391A 225 20708, 21385 OrfB of IS911 IS911; Escherichia coli 88 198/224 AAC70114
29 1,083 21303, 24554 Putative type II restriction enzyme, methylase subunit S. enterica serovar Typhimurium LT2 59 632/1060 NP 463354
30 894 24554, 27238 Putative cytoplasmic protein S. enterica serovar Typhimurium LT2 50 455/896 NP 463351
31 746 27251, 29491 Putative ATP-dependent Lon protease S. enterica serovar Typhimurium LT2 85 576/672 NP 463350
32 883 29535, 32186 Orf74 Plasmid pB171; Escherichia coli 25 235/920 NP 053136
33 traI 716 32341, 34491 Hypothetical protein Xylella fastidiosa 9a5c 26 94/353 NP 299042
34 606 34540, 36360 TraG Plasmid R27; S. enterica serovar Typhi 30 186/615 NP 458648
35 186 36370, 36930 Large repetitive protein S. enterica serovar Typhi CT18 25 20/78 NP 458558
36 214 36908, 37552 Hypothetical protein Plasmid R27; S. enterica serovar Typhi 29 29/98 NP 058330
37 195 38166, 37579 Hypothetical protein Listeria monocytogenes 24 30/123 NP 464171
39 traL 93 38455, 38736 Sex pilus assembly and synthesis protein Plasmid pNL1; Novosphingobium aromaticivorans 25 18/72 NP 049168
40 traE 130 38967, 39359 HtdE Plasmid R478; Serratia marcescens 25 29/115 AAL27019
41 traK 300 39340, 40242 HtdP Plasmid R478; Serratia marcescens 26 66/251 AAL27020
42 traB 429 40242, 41531 TrhB; putative transfer protein Plasmid R27; S. enterica serovar Typhi 40 84/209 NP 058242
43 htdD 216 41528, 42178 HtdD Plasmid R478; Serratia marcescens 28 45/158 AAD01915
44 traA 128 42175, 42561 TraA Plasmid R27; S. enterica serovar Typhi 24 21/85 NP 058247
45 106 42922, 42602 Putative acetyltransferase S. enterica serovar Typhimurium LT2 45 41/90 NP 463183
46 88 43365, 43099 Hypothetical protein Escherichia coli O157:H7 44 40/89 NP 289961
47 125 43920, 43543 SMA0431, hypothetical protein Rhizobium meliloti 27 31/114 Q930G9
48 tnp391B 305 45323, 44406 Transposase Listonella anguillarum 66 201/301 AAA81774
49 107 46010, 45687 Glycosyl transferase Streptomyces fradiae 22 21/95 AAF00214
50 82 46700, 46452 Hypothetical protein G Tn1404 Pseudomonas sp. strain R9 60 15/25 AAD47995
51 508 45742, 47268 Sulfate permease Tn1404 Pseudomonas sp. strain R9 80 401/497 AAD47994
52 283 47280, 48131 Hypothetical protein B Tn1404 Pseudomonas sp. strain R9 38 109/283 AAD47991
53 149 48604, 48155 Conserved hypothetical protein Pseudomonas aeruginosa 36 53/146 NP 250418
54 169 49144, 48635 Conserved hypothetical protein Pseudomonas aeruginosa 35 39/109 NP 249266
56 htdT 230 49588, 50280 HtdT; putative transfer protein Plasmid R27; S. enterica serovar Typhi 26 53/197 NP 058240
57 traC 799 50280, 52679 TraC Plasmid R27; S. enterica serovar Typhi 27 239/869 NP 058238
59 trhF 163 53024, 53515 TrhF Plasmid R27; S. enterica serovar Typhi 28 36/127 NP 058222
60 traW 375 53523, 54650 Putative transfer protein, pilus formation Plasmid R27; S. enterica serovar Typhi 27 84/303 NP 058221
61 traU 342 54634, 55662 TraU Plasmid pNL1; Novosphingobium aromaticivorans 36 125/339 NP 049157
62 traN 1,230 55665, 59357 TraN Genomic island STI1; S. enterica serovar Typhimurium 33 418/1253 AAK02035
64 220 59951, 60613 DNA ligase Escherichia coli O157:H7 25 31/124 NP 288973
65 200 61306, 60704 Lipoprotein Haemophilus ducreyi 21 30/139 AAB48950
66 112 61662, 62000 AnsG oxidoreductase Streptomyces collinus 27 19/68 AAD31836
67 139 62016, 62435 Single-strand binding protein Plasmid pLP231a; Escherichia coli 38 52/135 C38487
68 272 62515, 63333 Recombination protein Bet Bacteriophage 933W; Escherichia coli O157:H7 55 108/195 NP 049474
69 338 63621, 64637 Hypothetical protein Xylella fastidiosa 9a5c 32 51/155 NP 298936
70 358 64730, 65806 Probable cobalamin biosynthesis protein Sinorhizobium meliloti 30 87/281 NP 386778
71 255 65806, 66573 Molybdate metabolism regulator-related protein Deinococcus radiodurans 31 33/105 NP 386778
72 317 66672, 67625 Hypothetical protein Plasmid R27; S. enterica serovar Typhi 20 41/205 NP 058418
74 551 68197, 69852 Hypothetical protein Plasmid R27; S. enterica serovar Typhi 21 138/636 NP 058417
75 165 69938, 70435 RadC; putative DNA repair protein Vibrio cholerae 56 86/151 NP 231421
78 357 70867, 71940 Hypothetical protein Plasmid R27; S. enterica serovar Typhi 30 113/375 NP 058415
79 235 72030, 72737 Hypothetical protein SXT element; Vibrio cholerae 80 61/76 AAK95994
80 180 73088, 73630 Probable oxidoreductase Agrobacterium tumefaciens 27 35/126 NP 396434
81 traF 314 74368, 75312 TraF SXT element; Vibrio cholerae 97 306/314 AAK 95986
82 traH 462 75315, 76703 TraH Genomic island STI1; Salmonella enterica serovar Typhimurium 42 189/449 AAK02038
83 traG 1,189 76707, 80276 Putative pilus assembly protein Genomic island STI1; Salmonella enterica serovar Typhimurium 30 375/1214 AK02037
84 merR 129 80374, 80763 MerR IncJ element pMERPH; Shewanella putrefaciens 100 557/557
85 merT 107 80848, 81171 MerT IncJ element pMERPH; Shewanella putrefaciens 97 99/102 Q54462
86 merP 91 81256, 81531 MerP IncJ element pMERPH; Shewanella putrefaciens 98 90/91 Q54463
87 merC 137 81541, 81954 MerC IncJ element pMERPH; Shewanella putrefaciens 98 135/137 CAA89056
88 merA 557 81992, 83665 MerA; mercuric reductase IncJ element pMERPH; Shewanella putrefaciens 100 557/557 Q54465
89 143 84202, 83771 Hypothetical protein Listeria innocua 26 23/86 CAC42036
90 177 84790, 84257 FlhC; flagellar transcriptional activator S. enterica serovar Typhimurium LT2 27 41/150 AAB96640
91 99 85086, 84787 FlhD protein Serratia liquefaciens 28 28/97 S61276
92 182 85631, 85083 Hypothetical protein S. enterica serovar Typhi CT18 32 39/121 NP 458645
93 202 86226, 85618 Hypothetical transmembrane protein Ralstonia solanacearum 39 26/66 CAD17270
94 289 87136, 86267 Unknown protein Cryptic prophage CP-933M; Escherichia coli O157:H7 35 27/76 NP 286859
96 215 87561, 88208 Putative prophage repressor protein; similar to cI repressor Yersinia pestis 38 87/227 NP 404832
a

ORFs not showing significant homology to corresponding proteins in the public databases are not shown. Nucleotide position from start to stop codon in the R391 sequence. Identity in percentage and amino acids (number identical relative to total number examined) as determined with BLAST and FASTA.

b

Nucleotide position from start to stop codon in the R391 sequence.

c

Identity in percentage and amino acids (number identical relative to total number examined) as determined with BLAST and FASTA.