Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_007474367.1 CMTB2_RS04430 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q97GH9 (387 letters) >NCBI__GCF_000170735.1:WP_007474367.1 Length = 430 Score = 190 bits (482), Expect = 7e-53 Identities = 133/408 (32%), Positives = 215/408 (52%), Gaps = 45/408 (11%) Query: 15 VTFDKGEGTKLYDKDGNEYIDFVSGVAVNCLGHCNPSIVKAIEEQSSKLMHV-SNYYWNE 73 + KGEG L D DGN YID +S VN GHCNP I K I EQ + L HV + + Sbjct: 30 IPIKKGEGVYLEDFDGNRYIDAISSWWVNLFGHCNPYINKKITEQLNTLEHVIFAGFTHM 89 Query: 74 NAMELTEILCKNSEFDKVFMCNSGTEAIEAGLKLARKYALLHGDENKKEI----IYMDNS 129 A++L E +C ++ DKVF ++G+ A+E +K++ H +NK EI ++NS Sbjct: 90 PAVKLAERICNLTKMDKVFYADNGSSAVEVAIKMS-----FHYWKNKGEIRPLFFSLENS 144 Query: 130 FHGRTMGALSVTGQPKYQESFKPLIGAVKSVKFNDLDD---------------IKQKISS 174 +HG T+GALSV Y++++K ++ +K++ D I +K Sbjct: 145 YHGETIGALSVGDVGLYKDTYKEIL--IKNITIPIPKDKSEEETNKALRKARKIFEKYHK 202 Query: 175 KTAAVIVEP-IQGEGGIIPAKKEYLKLLRDLCDENNALLIFDEVQCGMGRVGSLFAYQKF 233 +T+A I+EP IQ G + +++K L++LC+E N I DE+ G GR GS+FA ++ Sbjct: 203 QTSAFIIEPLIQCAGYMKMHSAKFVKGLKNLCEEFNIHFIADEIAVGFGRSGSMFACEQA 262 Query: 234 EVVPDIVCIAKALGGGF-PIGAMLAKESVASSFVPGD-------HGNTYGGNPLACAVAI 285 ++ PD + ++K L GG+ P+ L + + +F H ++Y NPL CA A Sbjct: 263 KIKPDFMLLSKGLTGGYLPLSLCLTTDEIYQAFYCDYTELKAFLHSHSYTANPLGCAAAN 322 Query: 286 AVLKELVDKKVVEINVNEKSKYLFDKLMTLKEKYKVINDVRGMGLLIGVEV------ACD 339 A L + V+E N EKSKY+++ + KE V ++R G++ +E+ Sbjct: 323 ATLDIFEKENVIEKN-KEKSKYIWESIQKFKELPNV-KEIRQTGMITAIEMIDYPWQERK 380 Query: 340 VKKIINKCFESKLLLITAGKNVVRFLPPLNVSFEEIDKALGIFEESIK 387 ++ ++ +LL G NV+ F+PP ++ EEID+ + + E IK Sbjct: 381 GLQVYEYGLQNGVLLRPLG-NVIYFMPPYIINKEEIDRMINVAYEGIK 427 Lambda K H 0.318 0.137 0.395 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: 449 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: 387 Length of database: 430 Length adjustment: 31 Effective length of query: 356 Effective length of database: 399 Effective search space: 142044 Effective search space used: 142044 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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