TABLE 2.
Summary of computer analysis of nucleotide sequence of transfer region 1 from R27
| ORFa | Genea | Lengthb | Molc wt | pId | PSI BLAST resultse (protein/source/length of homolog) | Degree of relatednesse (identical residues/range of identity = % identity) | Accession no. of homologe | Motifsf |
|---|---|---|---|---|---|---|---|---|
| orf115 | 242 | 27.9 | 9.64 | ORF8 from Bacteriodes uniformis | 46/210 = 21% | AF238367 | None | |
| NBU1 element (246 aa) | ||||||||
| orf116 | 393 | 42.9 | 7.54 | Proteinase IV from Vibrio cholerae (616 aa) | 69/343 = 20% | H82130 | Type IV protease (191-325) | |
| orf117 | traJ | 220 | 25.4 | 9.61 | None | AraC transcriptional regulator (8-48) and leucine zipper (182-202) | ||
| orf118 | 367 | 42.2 | 8.15 | None | None | |||
| orf119 | traG | 694 | 80.0 | 8.61 | TraG from R751 (637 aa) | 70/539 = 12% (all in C-terminal end) | S22992 | Walker A (205-212) and Walker B (404-414) |
| orf120 | traI | 1,011 | 113.0 | 4.68 | None | Zinc carboxypeptidase (588-598) and relaxase motifs I-III | ||
| orf121 | 240 | 27.9 | 9.10 | None | None | |||
| orf122 | traH | 161 | 19.2 | 9.50 | None | None | ||
| orf123 | trhR | 266 | 30.3 | 5.15 | None | None | ||
| orf124 | trhY | 170 | 19.4 | 8.57 | None | None | ||
| orf125 | trhX | 95 | 11.0 | 4.91 | None | None | ||
| orf126 | trhF | 348 | 39.6 | 5.20 | TraF from R100 (247 aa) | 46/231 = 19% | AAB61943 | None |
| orf127 | trhH | 470 | 48.1 | 5.02 | TraH from R100 (460 aa) | 108/419 = 25% | BAA78879 | None |
| orf128 | trhG | 1,329 | 140.9 | 5.34 | TraG from F factor (938 aa) | 121/682 = 17% (all in N-terminal end) | AAC44184 | None |
a
Gene/ORF designation according to Sherburne et al. (30) or from this analysis.
b
Length in amino acid residues according to Sherburne et al. (30) or from this analysis.
c
Molecular (Mol) weight was predicted using the Compute pI/Mw tool (http://ca.expasy.org/tools/pi_tool.html).
d
pI values were predicted using the Compute pI/Mw tool (http://ca.expasy.org/tools/pi_tool.html).
e
Homologous proteins were identified with PSI-BLAST (http://www.ncbi.nlm.nih.gov/BLAST/).
f
Motifs were identified using Prosite (http://ca.expasy.org/tools/scnpsite.html) or alignment (Fig. 2).