TABLE 3.
Genetic features of the identified AGI-3 open reading frames
| ORF | G+C content (%) | Size (aa) | Positiona (bp) | Similarities with representative sequence in database (Blastp E value)b | Accession no. | Conserved domain | Predicated function |
|---|---|---|---|---|---|---|---|
| aec-33 | 45 | 394 | 598-1782 | Putative prophage integrase, E. coli CFT073 (0.0) | NP_756353.1 | cd00801 | Integrase |
| aec-34 | 46 | 347 | 2194-3237 | ShiA homolog, E. coli CFT073 (0.0) | NP_756354.1 | None | Reduction of inflammation |
| aec-35 | 44 | 356 | C 3635-4705 | Putative transcriptional regulator, E. coli CFT073 (0.0) | NP_756356.1 | smart00354, pfam00532 | Transcriptional regulator LacI family |
| aec-36 | 42 | 452 | 4910-6268 | Hexuronate transporter, E. coli CFT073 (0.0) | NP_756357.1 | pfam00083 | Sugar (and other) transport |
| aec-37 | 43 | 795 | 6277-8664 | Putative glucosidase, E. coli CFT073 (0.0) | NP_756359.1 | pfam01055 | α-Glycosidase |
| aec-38 | 55 | 151 | C 9306-9761 | IS1 protein InsB, E. coli EDL933 (3e-61) | AAG55747.1 | pfam03400 | Transposase |
| aec-39 | 53 | 91 | C 9680-9955 | IS1 ORFB, Shigella flexneri 2a str. 2457T (7e-42) | NP_836645.1 | pfam03811 | Transposase |
| aec-40 | 51 | 70 | C 9772-9984 | Putative iso-IS1 ORF, Shigella flexneri (5e-25) | AAK18551.1 | None | Unknown |
| aec-41 | 44 | 320 | C 10588-11550 | Putative fructokinase, E. coli EDL933 (9e-61) | NP_311269.1 | cd01167 | Fructokinase |
| aec-42 | 50 | 302 | C 11664-2572 | No significant similarities | |||
| aec-43 | 49 | 497 | C 12691-14184 | Glycosylhydrolase, Bacteroides thetaiotaomicron VPI-5482 (9e-37) | AAO76867.1 | smart00640 | Glycosylhydrolase |
| aec-44 | 46 | 420 | C 14199-15461 | No significant similarities | |||
| aec-45 | 56 | 477 | C 15558-16991 | Sucrose hydrolase, E. coli (e-152) | AAP79503.1 | smart00640 | Glycosylhydrolase |
| aec-46 | 49 | 412 | C 17011-18249 | Sugar transporter FruP, Bacillus megaterium (6e-98) | AAM19070.1 | pfam01306 | Sugar transporter |
| aec-47 | 52 | 311 | 18551-19486 | Putative sucrose-specific transcriptional regulator, Yersinia pestis KIM (2e-86) | NP_669120.1 | smart00354, pfam00532 | Transcriptional regulator |
| aec-48 | 49 | 127 | C 20425-20808 | (ORF truncated) Possible transposase remnant, Yersinia pseudotuberculosis IP 32953 (1e-60) | CAF25366.1 | pfam00665 | Transposase |
| aec-49 | 56 | 301 | C 20793-21698 | Hypothetical ORF in IS2, Klebsiella pneumoniae (e-162) | AAR07888.1 | pfam00665 | Transposase |
| aec-50 | 51 | 136 | C 21656-22066 | IS2 ORFA, Shigella flexneri 2a str. 2457T (3e-60) | NP_838126.1 | pfam01527 | Transposase |
| aec-51 | 53 | 225 | 22338-23015 | Unknown protein encoded by ISEc8, E. coli CFT073 (e-115) | NP_755534.1 | pfam01527 | Transposase |
| aec-52 | 55 | 115 | 23015-23362 | Unknown protein encoded by ISEc8, E. coli CFT073 (4e-60) | NP_755535.1 | pfam05717 | Transposase |
| aec-53 | 57 | 523 | 23382-24953 | IS66-like transposase, E. coli (0.0) | CAD33772.1 | pfam03050 | Transposase |
| aec-54 | 55 | 268 | C 25214-26020 | (ORF truncated) Putative arabinose exporter (MFS superfamily), Acinetobacter sp. ADP1 (3e-29) | YP_047119.1 | COG2814 | Carbohydrate transport and metabolism |
| aec-55 | 54 | 129 | C 26375-26764 | (ORF truncated) Oxidoreductase, aldo/ ketoreductase family, Silicibacter pomeroyi DSS-3 (3e-31) | YP_165172.1 | pfam00248 | Oxidoreductase |
| aec-56 | 52 | 247 | 26921-27664 | (Truncated ORF) IS100 transposase, Yersinia pestis (e-122) | YP_094025.1 | COG4584, partial cd00093 | Transposase |
| aec-57 | 55 | 132 | 27544-27942 | (Truncated ORF) Transposase for insertion sequence IS100, Yersinia pestis biovar Medievalis str. 91001 (e-71) | AAS60948.1 | Partial COG4584 | Transposase |
| aec-58 | 50 | 260 | 27939-28721 | Insertion sequence IS100, ATP-binding protein, Yersinia pestis biovar Medievalis str. 91001 (e-132) | NP_993067.1 | smart00382 | Transposase |
| aec-59 | 53 | 141 | C 28827-29252 | Hypothetical protein SF2980, Shigella flexneri 2a str. 301 (1e-69) | NP_708754.1 | None | Unknown |
| aec-60 | 55 | 129 | C 29249-29638 | Hypothetical protein SF2981, Shigella flexneri 2a str. 301 (1e-59) | NP_708755.1 | None | Unknown |
| aec-61 | 59 | 189 | C 29799-30368 | ORF31, E. coli RW1374 (3e-91) | CAI43834.1 | None | Unknown |
| aec-62 | 51 | 169 | 32482-32991 | ORF33, E. coli RW1374 (2e-96) | CAI43836.1 | None | Unknown |
| aec-63 | 45 | 500 | C 33313-34815 | Hypothetical protein YfjI, E. coli CFT073 (0.0) | NP_755527.1 | None | Unknown |
| aec-64 | 58 | 303 | 35989-36900 | YeeP protein, E. coli (e-162) | CAE85196.1 | COG3596 | GTP binding protein |
| aec-65 | 52 | 225 | C 37213-37890 | Putative transposase, E. coli RW1374 (e-129) | CAI43898.1 | pfam00665 | Transposase |
| aec-66 | 50 | 115 | C 38079-38426 | Unknown protein encoded by IS911 within prophage CP-933L, E. coli EDL933 (2e-46) | AAG58804.1 | pfam01527 | Transposase |
| aec-67 | 58 | 727 | 38411-40594 | (Truncated ORF) Adhesin AIDA-I precursor, E. coli (0.0) | BAA15832.1 | cd01344, pfam03797 | Autotransporter |
| aec-68 | 52 | 840 | 40709-43231 | ORF36, E. coli RW1374 (0.0) | CAI43839.1 | None | Unknown |
| aec-69 | 48 | 151 | 43307-43762 | Hypothetical protein c3665, E. coli CFT073 (2e-83) | NP_755540.1 | None | Unknown |
| aec-70 | 55 | 77 | 43841-44074 | ORF39, E. coli RW1374 (8e-37) | CAI43842.1 | None | Unknown |
| aec-71 | 57 | 272 | 44174-44992 | ORF40, E. coli RW1374 (e-146) | CAI43843.1 | pfam06067 | Unknown |
| aec-72 | 54 | 161 | 45047-45532 | ORF41, E. coli RW1374 (4e-84) | CAI43844.1 | pfam03230 | Antirestriction |
| aec-73 | 58 | 163 | 45533-46024 | YeeS protein, E. coli 536 (1e-74) | CAE85201.1 | pfam04002 | DNA repair protein |
| aec-74 | 53 | 73 | 46094-46315 | ORF44 (YeeT), E. coli RW1374 (5e-34) | CAI43847.1 | None | Unknown |
| aec-75 | 57 | 122 | 46478-46846 | Putative structural protein, E. coli EDL933 (4e-64) | AAG55773.1 | None | Unknown |
| aec-76 | 53 | 124 | 46936-47310 | ORF45, E. coli RW1374 (4e-66) | CAI43848.1 | None | Unknown |
| aec-77 | 51 | 162 | 47307-47795 | YeeW, E. coli RW1374 (5e-87) | CAI43849.1 | None | Unknown |
| aec-78 | 50 | 80 | 47762-48004 | ORF104, E. coli RW1374 (1e-29) | CAI43905.1 | None | Unknown |
| aec-79 | 48 | 281 | 48089-48934 | Z1226 protein, E. coli 536 (e-151) | CAD33792.1 | None | Unknown |
| aec-80 | 39 | 135 | 48980-49387 | (Truncated ORF) Hypothetical protein c4580, E. coli CFT073 (5e-34) | NP_756440.1 | Partial COG3943 | Unknown |
| aec-81 | 34 | 122 | 49530-49898 | Hypothetical protein c4581, E. coli CFT073 (3e-36) | NP_756441.1 | None | Unknown |
a
C indicates ORFs transcribed on the complementary strand.
b
str., strain; MFS, major facilitator superfamily.