Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_022947828.1 H035_RS0104615 aspartate aminotransferase family protein
Query= curated2:Q81M98 (386 letters) >NCBI__GCF_000421465.1:WP_022947828.1 Length = 463 Score = 225 bits (574), Expect = 2e-63 Identities = 145/402 (36%), Positives = 209/402 (51%), Gaps = 46/402 (11%) Query: 16 FVKGNGTKVIDNNGKQYLDFTSGIGVCNLGHCHPTVMKAVQEQLN---------DIWHIS 66 + G + D +YLD SG GV LG HPT+ A++E L+ D+ +S Sbjct: 41 YTHARGPYLYDQEDNEYLDLLSGFGVFALGRNHPTIQSALREVLDLDLPDLVQMDVSILS 100 Query: 67 NLFTNSLQEEVASLLTENIALDYVFFCNSGAEANEAALKLARKHTGKSLVVTCEQSFHGR 126 L L + LT+ +FFCNSGAEA EAA+K AR TG+S ++ CE +FHG Sbjct: 101 GLLAEKLVQVTPEPLTK------LFFCNSGAEAVEAAIKFARYTTGRSRILYCEHAFHGL 154 Query: 127 TFGTMSATGQNKVKEGFGPLLPSFLHTPFNDIKALKEVMNEE-VAAVMVEVVQGEGGVIP 185 T G +S G+ ++GFGPLLP PFND++AL+ + E+ AA +VE +QG+G +P Sbjct: 155 TLGALSLNGEEVFRQGFGPLLPDCDAIPFNDLEALERALKEQPTAAFIVEPIQGKGVNLP 214 Query: 186 ADLSFLKEIETLCKKFGSLFIIDEVQTGIGRTGTLFAYEQMGIDPHIVTTAKALGNG-IP 244 D +L E LC+K+G+LFI DE+Q G+GRTG L+A E G++P ++ AKAL G +P Sbjct: 215 DD-DYLTEAARLCRKYGALFIADEIQAGLGRTGRLWAIEHWGVEPDMLLMAKALSGGFVP 273 Query: 245 VGAM-----IGRKELGTSFTAGSHGSTFGGNYVAMAAAKEVLQVSKRLSFLKEVQEKGEY 299 VGA+ + K A HGSTF N AMAA L V + L +GE Sbjct: 274 VGAVAMTAHVMDKVFNRMDRAVVHGSTFSKNNPAMAAGLATLSVIEEEKLLANAARQGEA 333 Query: 300 VLQKLQEELQHVECIQNIRGKGLMVGIE------CTHEVASFIEQLEKEGLL-------- 345 ++ L E Q +RGKGLM+ +E + A + + +GL Sbjct: 334 LIGGLNALTDKYEFFQAVRGKGLMLALEFGKPRSLKLKTAWSLLETANKGLFSQMVTIPL 393 Query: 346 ---------VLQAGPNVIRLLPPLIVTNEELEQAVYMIKKVV 378 V G NV++ LPPL++ +++E V + V+ Sbjct: 394 FKRHRILSQVAGHGMNVVKFLPPLVIGAKDVEWIVSAMDDVL 435 Lambda K H 0.319 0.136 0.388 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: 363 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 386 Length of database: 463 Length adjustment: 32 Effective length of query: 354 Effective length of database: 431 Effective search space: 152574 Effective search space used: 152574 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 (21.7 bits) S2: 50 (23.9 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