Align Acetylornithine aminotransferase 1; ACOAT 1; EC 2.6.1.11 (uncharacterized)
to candidate 201879 SO2741 adenosylmethionine--8-amino-7-oxononanoate aminotransferase (NCBI ptt file)
Query= curated2:Q89VE9 (405 letters) >FitnessBrowser__MR1:201879 Length = 461 Score = 161 bits (408), Expect = 3e-44 Identities = 126/421 (29%), Positives = 206/421 (48%), Gaps = 50/421 (11%) Query: 13 LPVFARSDLGFERGEGCWLIATNGDRYLDFTSGVAVNALGHAHPALVKALQEQATKLWHM 72 LPVF G +GC L +G + +D TS G+ HPA++ A+++Q +L H+ Sbjct: 25 LPVF-----GVHSAQGCELELVDGRKLIDGTSSWWACVHGYGHPAILTAMEQQLHQLSHV 79 Query: 73 SNLFQSPDGEKLATRLCNESFA------DFVFFCNSGAEALEGVIKLVRHHHFSKGHP-- 124 +F E A LC + A VF C+SG+ A+E IK+ + + P Sbjct: 80 --MFGGITHEP-AIELCKKLLAMTCEPLTKVFLCDSGSIAVEVAIKMALQYWQGQDLPLA 136 Query: 125 ---ERYRIITFEGAFHGRTLATLAAT----------GSAKYLEGF-GPPMDGFDQVPHGD 170 ++ RI+T + +HG T A ++ G A + F P F + H D Sbjct: 137 QKAQKQRILTVKKGYHGDTFAAMSVCDPEGGMHTMFGEAVIKQCFVDAPQTPFGESLHQD 196 Query: 171 ----IEAVKKAIGPQTAGILIEPI-QGEGGVRSATPAFLKALRQLCDEKGLLLAFDEVQT 225 ++ + + A ++IEPI QG GG+R + +L+ LR LCDE +LL DE+ T Sbjct: 197 DLAPMQRILREQHQDIAAVIIEPIMQGAGGMRFYSSEYLRGLRALCDEYNVLLILDEIAT 256 Query: 226 GMGRTGDLFAHRRTGVTPDVMSLAKALGGGF-PIGAILATADAAAGM-----GPGSHGST 279 G GRTG LFA+ T +TPD++ L KAL GG+ + A L T + A G+ G HG T Sbjct: 257 GFGRTGKLFAYEHTDITPDILCLGKALTGGYISLAATLCTDNVAQGISQSPAGVFMHGPT 316 Query: 280 FGGNPLAIAAANAVLDVMLKPGFFDHVQKMSLLLKQKLASVIDRHGDVVSEVRGEGLLIG 339 F GNPLA AAA A LD++ + + V + ++++LA ID + V+ +L Sbjct: 317 FMGNPLACAAACASLDLINQQEWPAQVAAIEQQMQRELADAID-----IPSVKAVRVLGA 371 Query: 340 IKAVVPSGDLVAALRNEKLLTVGAG----DNVVRFLPPLIVTEAEIEDSVGRLERACAAI 395 + + + A ++ + +G N++ +PP +++ A++ +++ A I Sbjct: 372 VGVLEMHQAVNTAALQQQFVDLGVWVRPFANLIYIMPPYVISSAQLSQLTQAMKQVAATI 431 Query: 396 S 396 + Sbjct: 432 T 432 Lambda K H 0.320 0.137 0.404 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: 429 Number of extensions: 21 Number of successful extensions: 5 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: 405 Length of database: 461 Length adjustment: 32 Effective length of query: 373 Effective length of database: 429 Effective search space: 160017 Effective search space used: 160017 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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