TABLE 2.
Predicted rRNA and protein coding genes in marine crenarchaeal fosmid 4B7a
| 74A4# | Nucleotide range (protein size, in no. of amino acids) | Dir | Predicted function | Most similar homolog (e-value) | Apparent phylo-genetic affinity | Comments |
|---|---|---|---|---|---|---|
| 1 | 371–1459 (363) | + | Damage-induced, low-processivity DNA polymerase IV (DinB family) | 1706953_SULSO (5e-48) | Crenarchaeotal (Sulfolobus) or bacterial | So far not found in other archaea |
| 2 | 1449–2384 (312) | − | Uncharacterized multitransmembrane protein | None | NA | |
| 3 | 2426–3580 (385) | − | Uncharacterized conserved protein | 5457859_PYRAB (4e-71) | Euryarchaeotal | Protein family so far detected only in archaea; highly conserved paralog of 74A4#7 |
| 4 | 3671–4588 (306) | + | Periplasmic solute-binding protein | 7472739_DEIRA (3e-38) | Bacterial or euryarchaeotal | So far found only in archaea; highly conserved paralog of 74A4#6 |
| 5 | 4765–5034 (90) | − | Small membrane protein | None | NA | |
| 6 | 5246–5914 (223) | − | Periplasmic disulfide bond isomerase | 2649220_ARCFU (2e-16) | Euryarchaeotal or bacterial | Among archaea, found only in Archaeoglobus |
| 7 | 6272–7624 (451) | + | DEAD family RNA helicase | 10175004_BACHA (3e-73) | Bacterial or euryarchaeotal | Among archaea, found only in Methanobacterium |
| 8 | 7673–7906 (78) | + | Transcriptional regulator of the AsnC family | 3257044_PYRHO (3e-08) | Euryarchaeotal | |
| 9 | 8294–8734 (147) | + | Uncharacterized protein | None | NA | |
| 10 | 8769–9530 (254) | + | Uncharacterized secreted (periplasmic) protein | None | NA | |
| 11 | 9566–9847 (94) | + | Uncharacterized membrane protein | None | NA | |
| 12 | 9885–10202 (106) | + | Uncharacterized protein | None | NA | |
| 13 | 10205–12226 (674) | − | Highly conserved protein containing a thioredoxin domain | 586842_BACSU (e-141) | Bacterial | More distant homologs are seen in archaea |
| 14 | 12502–13218 (239) | − | Uncharacterized multitransmembrane protein | None | NA | |
| 15 | 13459–15651 (731) | − | EF2 | 461998_SULSO (0.0) | Crenarchaeotal | |
| 16 | 16479–16907 (143) | − | Uncharacterized protein | None | NA | Distantly related to the N-terminal portion of 4B7#19 |
| 17 | 17253–17567 (105) | − | Rhodanese-related sulfurtransferase or oxidoreductase | 1723283_SCHPO (2e-06) | Uncertain | So far not found in crenarchaeotes |
| 18 | 17595–17975 (127) | + | Uncharacterized protein | None | ||
| 19 | 17976–18818 (281) | − | Type I membrane protein containing a C-terminal cytoplasmic J domain (DnaJ) | 544179_METMA (2e-12) | Euryarchaeotal or bacterial | Unique domain architecture |
| 20 | 19397–21106 (570) | − | SWI/SNF family helicase | 3329163_CHLTR (1e-43) | Bacterial | Distinct subfamily of SWI/SNF helicases so far not seen in archaea |
| 21 | 21169–21903 (240) | − | Uncharacterized protein homologous to the N-terminal domain of Lon protease | 11354694_VIBCH (2e-08) | Bacterial | Domain potentially involved in proteolysis regulation; so far found in bacteria and eukaryotes but not in archaea |
| 22 | 21970–22482 (173) | + | Uncharacterized coiled-coil protein | None | NA | |
| 23 | 22485–23483 (333) | + | Bifunctional protein: biotin repressor and biotin (acetyl-CoA carboxylase) ligase | 773349_BACSU (1e-45) | Bacterial or euryarchaeotal | Typical bacterial domain architecture, with N-terminal DNA-binding domain and C-terminal enzymatic domain |
| 24 | 23549–25069 (507) | + | Secreted (periplasmic) Zn-dependent protease containing TPR repeats | 2688100_BORBU (3e-07) (TPR repeats), 5921827_RATNO (0.002) (protease) | Uncertain | The TPR repeats most closely resembles those found in euryarchaeotes; no close homologs of the predicted protease; paralog of 74A4#15 |
| 25 | 25072–25647 (192) | − | Ferritin (nonheme iron-containing protein) | 1707687_SULSO (e-49) | Crenarchaeotal | |
| 26 | 26062–26694 (211) | + | Transcription factor IIB | 1729909_SULSH (9e-52) | Crenarchaeotal | |
| 27 | 26866–27213 (116) | + | Uncharacterized nonglobular protein | None | NA | |
| 28 | 27359–27661 (101) | + | Uncharacterized protein | None | NA | |
| 29 | 27735–27956 (74) | − | Small membrane protein | None | NA | Paralog of 74A4#3 |
| 30 | 28121–28312 (64) | + | RNA-binding cold shock protein | 3097243_MYCLE (2e-13) | Bacterial | So far not seen in other archaea |
| 31 | 23S RNA | |||||
| 32 | 16S RNA | |||||
| 33 | 28470–28673 (68) | + | Small Cys- and His-rich protein | None | NA | Potentially involved in metal-dependent nucleic acid binding |
| 34 | 33434–34744 (437) | + | Glutamate-1-semialdehyde aminotransferase | 3599375_CENSY (e-158) | Euryarchaeotal or crenarchaeotal | Highly conserved paralog of 74A4#24 |
| 35 | 34782–35432 (217) | + | NAD (P) H-flavin oxidoreductase | 3915352_ARCFU (4e-11) | Euryarchaeotal | |
| 36 | 35435–35830 (158) | − | Uncharacterized membrane protein | None | NA | Paralog of 74A4#19 |
| 37 | 35989–36483 (165) | − | Uncharacterized conserved protein | 6015921_SULSO (2e-21) | Crenarchaeotal | Found in archaea and eukaryotes |
| 38 | 36518–37099 (194) | − | Uncharacterized protein | None | NA | |
| 39 | 37092–39980 (963) | − | Very large secreted (periplasmic) protein | None | NA | |
| 40 | 40120–40311 (64) | − | Zn ribbon protein | None | NA | Potentially involved in metal-dependent nucleic acid binding |
| 41 | 40653–41327 (225) | + | Methionine aminopeptidase | 3257034_PYRHO (3e-40) | Euryarchaeotal |
a
See footnotes to Table 1.