Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 8500245 DvMF_1002 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__Miya:8500245 Length = 491 Score = 219 bits (557), Expect = 2e-61 Identities = 148/424 (34%), Positives = 223/424 (52%), Gaps = 57/424 (13%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYY-N 77 P+ + EG R+ D +G Y+D V+ + NV GH HP + A++ Q++++ H + L + Sbjct: 50 PLVIGAAEGNRLTDTDGVSYLDGVSSLWTNVHGHRHPRLDAAIRAQLDKVAHTTLLGLGS 109 Query: 78 EPQAEAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF-----------TGCTKFIA 126 EP E A LA AP+ L +VF+ +SG+ SVE A+K+A +F T+F++ Sbjct: 110 EPSIELAARLAAIAPQGLTRVFYSDSGSTSVEVALKIAFQFHRQAPAHLGGDARRTRFLS 169 Query: 127 FEGGFHGRTMGALSATWKPEFREPFEPLV--------PEFEHVPYG-DVNAVEKAI---- 173 +HG T+GA++ F + PL+ P P+G + E+ Sbjct: 170 LRNAYHGDTVGAVALGGMALFHSIYAPLLFDTVKAESPYCYRCPFGRQAGSCERECITHM 229 Query: 174 -------DDDTAAVIVEP-VQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRT 225 + A +VEP VQG AG+ + P G+LR +RELCDEHG+ L+ DEV G G+T Sbjct: 230 ETLFARHGHELCAAVVEPLVQGAAGMLLQPPGWLRRVRELCDEHGVFLVADEVAVGFGKT 289 Query: 226 GQFFAFEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAF-------EPGDHGSTFGG 277 G FA E E V PD +CLAKG+ GG +P+ AT+ E V + F HG T+ G Sbjct: 290 GTLFACEQEGVTPDFLCLAKGISGGYLPLAATLTTERVHDGFLARHEELRTFFHGHTYTG 349 Query: 278 NPLACAAVCAAVSTVLEENLPEAAERK-GKLAMRILSEAEDV--VEEVRGRGLMMGVEVG 334 NPLACAA A++ EE + E + K +LA R L D+ V ++R RG+M G+E+ Sbjct: 350 NPLACAAAIASLDVFEEERVMERLQPKIARLAAR-LDTLRDLPHVGDIRQRGVMTGIEMV 408 Query: 335 DDERAKD-----------VAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELAD 383 + K+ V E RG ++ GDV+ L+PPL I +DE++ + + Sbjct: 409 RNRATKEAYDLALRVGHRVTLEARRRGVIIR-PLGDVMVLMPPLSITDDEIDLLVGATGE 467 Query: 384 ALRA 387 A+RA Sbjct: 468 AIRA 471 Lambda K H 0.318 0.137 0.405 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 462 Number of extensions: 22 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 389 Length of database: 491 Length adjustment: 32 Effective length of query: 357 Effective length of database: 459 Effective search space: 163863 Effective search space used: 163863 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory