Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_014149527.1 MEALZ_RS15150 aspartate aminotransferase family protein
Query= curated2:Q9K8V5 (384 letters) >NCBI__GCF_000968535.2:WP_014149527.1 Length = 463 Score = 236 bits (601), Expect = 1e-66 Identities = 147/393 (37%), Positives = 210/393 (53%), Gaps = 38/393 (9%) Query: 20 GTKLYDNQGNEYLDFVSGIAVCNLGHCHPKVVAAVEEQLHSFWHVSNLFHIPIQ--ENVA 77 G LYD QGNEYLD +SG V +G HP V++A++E L + NL + + + Sbjct: 46 GQYLYDEQGNEYLDLLSGFGVFAIGRNHPTVISALQETLTL--ELPNLVQLDVSILSGLL 103 Query: 78 A---LLTEQSGMDAVFFCNSGAEANEAAIKLARKATGKHEIVTFTQSFHGRTLGTMSATG 134 A L T ++ +FFCNSG EA EAAIK AR T + +IV +HG T+G +S G Sbjct: 104 AKEILTTTPENLEKMFFCNSGTEAVEAAIKFARYTTKRAKIVYCEHGYHGLTMGALSLNG 163 Query: 135 QDKIKTGFGPMLETFHHVPFNDIAALKQVV-NEQTAAIVLEVIQGEGGVNLIDPEFAASV 193 + + GFGP+L +PFND+AAL+Q + N+ AA ++E IQG+ GVNL D + V Sbjct: 164 EKIFREGFGPLLPDCIAIPFNDLAALEQALSNKDVAAFIVEPIQGK-GVNLPDDNYLVEV 222 Query: 194 NHVCQEHGILLIIDEIQTGIGRTGTAFAFQQYELTPDIITVAKGLGNGF-PVGAMLGKQH 252 +C+++G L + DEIQTGIGRTG +A Y PD+I ++K L GF PVGA+ QH Sbjct: 223 ERLCKKYGTLFVADEIQTGIGRTGKFWAIDHYGAKPDMILMSKALSGGFVPVGAVAMTQH 282 Query: 253 LIDAF-----SAGSHGSTFGGNPLAMAAAQAVLTEVFQPNFLQAVQEKGKQLLSGLNEAL 307 ++D A HGSTF N +AMAA A L + N ++ G +++ LN Sbjct: 283 IMDTVFNRMDRAVVHGSTFSKNNMAMAAGLAGLEVIKSENLVEQSATVGNDIIASLNALS 342 Query: 308 SGLEIVKEIRGNGLLVGIELQEEGAPFIK------QLREKGLL----------------- 344 + E +KE RG G ++ IE Q + +K + KGL Sbjct: 343 TKYEFLKEARGKGSMIAIEFQAPKSLTLKAAWAMLEAANKGLFCQMITIPLFKDHRILTQ 402 Query: 345 VLNAGPNVIRLLPPLVVTSEELHEAVTQLKEVL 377 V G NV++LLPPL +T ++ V + + Sbjct: 403 VAGHGMNVVKLLPPLTLTQKDRDHIVNAFDQTI 435 Lambda K H 0.318 0.135 0.391 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: 464 Number of extensions: 26 Number of successful extensions: 6 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: 384 Length of database: 463 Length adjustment: 32 Effective length of query: 352 Effective length of database: 431 Effective search space: 151712 Effective search space used: 151712 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