Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_017598182.1 D471_RS0108275 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q187D4 (421 letters) >NCBI__GCF_000341125.1:WP_017598182.1 Length = 405 Score = 234 bits (597), Expect = 4e-66 Identities = 131/408 (32%), Positives = 226/408 (55%), Gaps = 41/408 (10%) Query: 20 PRVLPLYQSTTFKYSSIDQLAELFDLKVDGHIYSRISNPTIQAFEEKISLLEGG-----V 74 P +P++++TT+++ + + A++ +G+ Y+RI +PT+ AF E ++ LEG V Sbjct: 29 PMRMPVHRATTYEFHTSQEYADVLAGTQEGYSYARIDSPTVDAFAEGVAALEGAGLRTRV 88 Query: 75 SSVAVSSGQSANMLAVLNICKSGDSILCSSKVYGGTFNLLGPSLKKFGIDLISFDLDSSE 134 A +SG +A ++ + ++G ++ + +YG T +LLG L++FG+ D+ + Sbjct: 89 RGQAFASGMAAISTVLMALTEAGAHVVAARSIYGNTHSLLGGLLRRFGVRTDFVDV-TDL 147 Query: 135 DEIVELAKENTKVVFAETLANPTLEVIDFEKIANVAKRINVPFIVDNSLASPVLCNPLKY 194 D + + +T V+F ETL+NPT+ V D ++A +A+ +VD++ ASPV+C PL++ Sbjct: 148 DAVRAAVRPDTAVLFTETLSNPTMAVSDLPELARIAREAGATLVVDSTFASPVVCRPLEH 207 Query: 195 GANIVTHSTTKYLDGHASSVGGIIVDGGNFNWDNGKFPELVEPDPTYHGISYTQKFGNAA 254 GA++V HS TK++ GH+ + GG+ V PEL++ Sbjct: 208 GADVVVHSATKFIGGHSDATGGVAVAA----------PELID------------------ 239 Query: 255 YATKARVQLLR-DYGNCLSPFNAYLTNLNVETLHLRMERHSENALKIARFLEKHENVDWI 313 R++ R D G CL+P AYL + +ETL LR+ R E+A A LE H V+ + Sbjct: 240 -----RIRAARIDLGPCLAPDEAYLLHRGLETLPLRVARQCESAAAFAAALEGHSAVERV 294 Query: 314 NYPGLEDNKYYENAKKYLSRG-CSGVLSFGVRGGLENAKKFVEKLQIASLVTHVSDVRTC 372 ++P L + E A K G C V++ RGG E +F +++++ ++ + T Sbjct: 295 DHPSLASHPQTELAAKLFDAGRCGAVVTVHPRGGQEAGMRFADRIRLGTVAASLGGTHTL 354 Query: 373 VIHPASTTHRQLTEEQLIASGVLPSLIRLSVGIENVEDLIADLNQALN 420 V H ASTTHRQ++E +L +G+ P +R S+G+E+ +DLI D AL+ Sbjct: 355 VGHVASTTHRQMSETELADAGISPGAVRFSIGLEDPQDLIDDALAALD 402 Lambda K H 0.316 0.135 0.387 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: 369 Number of extensions: 14 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: 421 Length of database: 405 Length adjustment: 31 Effective length of query: 390 Effective length of database: 374 Effective search space: 145860 Effective search space used: 145860 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 (21.6 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