Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 350970 BT1442 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file)
Query= curated2:P63566 (403 letters) >FitnessBrowser__Btheta:350970 Length = 804 Score = 159 bits (403), Expect = 2e-43 Identities = 127/402 (31%), Positives = 203/402 (50%), Gaps = 37/402 (9%) Query: 8 HPLYDTYNRAAL-RFERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQAEK 66 HP T + + + +R +G + EDG I+ + G++HP L + K Q +K Sbjct: 394 HPYTSTTDPLPVYKVKRADGATITLEDGRTLIEGMSSWWCAVHGYNHPVLNQAAKDQLDK 453 Query: 67 LWHL--SNVYEIPAQEKLGRRLVEST--FADKVFFTNSGAEALECAIKTARRYQYVSGHP 122 + H+ + PA E LG+ L+ K+F+ +SG+ A+E A+K A +Y Y +G P Sbjct: 454 MSHVMFGGLTHDPAIE-LGKLLLPLVPPSMQKIFYADSGSVAVEVALKMAVQYWYAAGKP 512 Query: 123 ERFRIITFEGAFHGRTLATIAAG----------GQAKYLEGFGPKVEG-FDQVPFGDEAA 171 ++ +T +HG T ++ G + + F P FD DE Sbjct: 513 DKNNFVTIRSGYHGDTWNAMSVCDPVTGMHSLFGSSLPVRYFVPAPSSRFDGEWNPDEII 572 Query: 172 -LRAAI---TPETAGILLEPI-QGEGGLRAFPEEFLRLVRQICDENGLLLLLDEVQTGVG 226 LR I + E A ++LEPI QG GG+ + ++LR ++C E+ +LL+ DE+ TG G Sbjct: 573 PLRETIEKHSKELAALILEPIVQGAGGMWFYHPQYLREAEKLCKEHDILLIFDEIATGFG 632 Query: 227 RTGKLFAHEWAGIRPDIMAIAKGIGGGF-PIGACLATAEAAKGMT-----AGMHGTTYGG 280 RTGKLFA E AG+ PDIM I K + GG+ + A LA+ + A ++ A MHG T+ G Sbjct: 633 RTGKLFAWEHAGVEPDIMCIGKALTGGYMTLSAVLASNQIADTISNHAPKAFMHGPTFMG 692 Query: 281 NPLGMAVGNAVLDVVLADGFMENVQATALVMKQGLASLVDRYPNVVSEIRGRGLLMGLKC 340 NPL AV A + ++L G+ ENV+ +K+ LA ++P V+++R +L + Sbjct: 693 NPLACAVACASVRLLLDSGWAENVKRIEAQLKEELAP-ARKFPQ-VADVR---ILGAIGV 747 Query: 341 VVPNTSLIQALRDEHILSVGAG----DNVVRLLPPLITTPEE 378 + S+ A + G +V L+PP I +PE+ Sbjct: 748 IQTERSVSMAYMQRRFVEEGIWVRPFGKLVYLMPPFIISPEQ 789 Lambda K H 0.320 0.138 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: 692 Number of extensions: 37 Number of successful extensions: 4 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: 403 Length of database: 804 Length adjustment: 36 Effective length of query: 367 Effective length of database: 768 Effective search space: 281856 Effective search space used: 281856 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: 53 (25.0 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