TABLE 1.
Annotated ORFs of Tn5253
| ORF (no. of amino acids)a,b | Annotation and comments; reference | Pfam domain(s)c (amino acids) [E value(s)] | Homologous protein ID/origin | No. of amino acids identical/total (%)-no. similar/total (%) | E valued |
|---|---|---|---|---|---|
| repA/orf2 (259) | Plasmid replication initiator protein A, N terminal; 20 | RepA_N (13-88) [4.1e-28] | |||
| orf4 (452) | DNA cytosine methyltransferase; 21 | ||||
| orf8 (195) | Protease, putative | Abi-CAAX protease self-immunity (103-188) [1.6e-13] | |||
| orf9 (196) | Abortive infection protein AbiEi; 22 | DUF4095 (29-146) [2.1e-23] | AAB52382.1/pNP40 L. lactis | 53/203 (26)-91/203 (44) | 6e-06 |
| orf10 (278) | Abortive infection protein AbiEii; 22 | DUF1814 (37-260) [2.1e-19] | AAB52383.1/pNP40 L. lactis | 81/279 (29)-136/279 (48) | 3e-18 |
| traG/orf13 (625) | TraG-like protein, involved in bacterial conjugal transfer; 23 | T4SS-DNA_transf (133-574) [1.1e-66] | |||
| orf15 (284) | Membrane protein, putative | TrbL (123-269) [0.00026] | YP_195781.1 (prgH)/pCF10 E. faecalis | 88/261 (33)-150/261 (57) | 5e-24 |
| orf16 (119) | Type IV secretion system protein | PrgI (4-95) [2.1e-22] | |||
| orf17 (785) | Type IV secretion protein, VirB4, ATPase | AAA_10 (449-736) [3.8e-44] | YP_195783.1 (prgJ)/pCF10 E. faecalis | 284/750 (37)-448/750 (59) | 5e-134 |
| orf18 (937) | Peptidoglycan hydrolase, putative | CHAP (805-926) [8.1e-30] | |||
| orf20 (64) | ISSth5, transposase, IS110 family, truncated | YP_139721.1/S. thermophilus | 43/64 (67)-47/64 (73) | 1e-13 | |
| orf43 (243) | ABC transporter: ATP-binding protein, putative | ABC_tran (27-173) [2.8e-30] | |||
| orf44 (438) | ABC transporter: permease (10 transmembrane helices predicted) | FtsX (55-176) [4.7e-07] | |||
| orf47 (2028) | Restriction-modification protein, putative | Methyltransf_26 (504-615) [1e-17], SNF2_N (1253-1600) [2.3e-14], Helicase_C (1698-1768) [2.2e-05] | |||
| orf52 (361) | DNA primase, putative | DUF3991 (113-198) [2e-13], Toprim_2 (203-329) [4.7e-10] | |||
| pezA/orf56 (158) | Antitoxin (TA system); 18 | ||||
| pezT/orf57 (252) | Toxin (TA system); 18 | ||||
| cat/orf60 (216) | CATe | CAT (1-205) [2.8e-95] | NP_040437.1/pC194 S. aureus | 216/216 (100) | |
| orf63 (281) | Plasmid replication protein | Rep_1 (54-250) [1e-48] | NP_040435.3/pC194 S. aureus | 194/195 (99)-195/195 (100) | 6e-111 |
| nplT/orf65 (245) | Truncated neopullulanase (α-amylase); 24 | Alpha-amylase (2-141) [5.5e-25] | |||
| pezA/orf67 (158) | Antitoxin (TA system); 18 | ||||
| pezT/orf68 (256) | Toxin (TA system); 18 | ||||
| umuD/orf69 (227) | UmuD MucA homolog; 25 | HTH_3 (7-61) [2.3e-17], Peptidase_S24 (143-205) [8e-12] | |||
| umuC/orf70 (471) | SOS response UmuC protein; 25 | IMS (17-207) [2.2e-17], IMS_HHH (223-255) [5.1e-06], IMS_C (268-382) [5.9e-12] | |||
| orf74 (121) | Bacterial mobilization protein, putative; 26 | MobC (60-107) [5.4e-15] | |||
| orf75 (609) | Relaxase; 27 | Relaxase (12-264) [1.6e-73] | |||
| orf76 (75) | Transcriptional regulator, putative; 28 | HTH_3 (5-60) [2.1e-15] | |||
| xis/orf78 (77) | DNA excisionase; 29 | AAA72427.1/Tn5276 L. lactis | 26/60(43)-43/60 (71) | 5e-06 | |
| int/orf79 (502) | DNA integrase; 30 | Phage_integrase (188-394) [2.3e-24] | NP_150133.1/bacteriophage MM1 S. pneumoniae | 121/413 (29)-193/413 (46) | 4e-26 |
a
The number of amino acids is shown in parentheses.
b
orf21 through orf42 correspond to orf1 to orf22 of Tn5251 and are annotated elsewhere (11). orf58 through orf68 belong to Ωcat(pC194).
c
The numbers in parentheses represent the part of the protein homologous to the Pfam domain.
d
Determined by compositional matrix adjustment.
e
CAT, chloramphenicol acetyltransferase.