Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_026605697.1 METAC_RS0101630 O-acetylhomoserine aminocarboxypropyltransferase
Query= metacyc::MONOMER-17873 (438 letters) >NCBI__GCF_000427445.1:WP_026605697.1 Length = 437 Score = 598 bits (1543), Expect = e-176 Identities = 291/420 (69%), Positives = 345/420 (82%), Gaps = 1/420 (0%) Query: 16 DTLALHGGSYRADPTTGAVAVPIYQTTSYQVHDTAHAARLAGLEEIGFAYTRIGNPTQDA 75 +TLALH G +RADPTTGAVAVPIYQTTSYQ HDT HAA L L+E+G YTRIGNPT D Sbjct: 9 ETLALHAG-WRADPTTGAVAVPIYQTTSYQFHDTQHAADLFALKELGNIYTRIGNPTVDV 67 Query: 76 FEQRLAALEGGVAALALASGQAASAIAVLTLAQAGDNIVTSTDLYGGTWNLFANTLRTLG 135 E+R+AALEGGVAALALASGQAASA +V LA+AGDNIV+STDLYGGTWNLFANTL+ G Sbjct: 68 LEKRIAALEGGVAALALASGQAASAFSVQNLARAGDNIVSSTDLYGGTWNLFANTLKDQG 127 Query: 136 IEARFVDPADPEAFRRATDARTRLYYGETLPNPKLTVFPIAEVAAIGRSLGVPLIIDNTA 195 IE RFVDP+DPE FRRATDARTR YY ETLPNPKL VFPIAEVAAIGRS G+PLI+DNTA Sbjct: 128 IEVRFVDPSDPENFRRATDARTRAYYAETLPNPKLIVFPIAEVAAIGRSFGIPLIVDNTA 187 Query: 196 TPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGAIIDGGTFPWADHAERHALLTGPEPSYH 255 P++ RP +HGAA+VVYS TKY+GGHG +IGG I+DGG F W ER L P+PSYH Sbjct: 188 APVLCRPLEHGAAIVVYSATKYLGGHGNSIGGLIVDGGNFDWEGFKERQPALNTPDPSYH 247 Query: 256 NASWTDLAAPFGPLAYILRARAGVLRDLGASIAPVSAFNLIQGLETLPLRLARHNANAIK 315 A WT+ P GP+AYI++AR +LRDLGA+++P +AF ++QG+E+L LR+ RH+ NA Sbjct: 248 GAVWTEAVKPLGPVAYIIKARTTLLRDLGAALSPFNAFLILQGVESLALRIERHSKNAET 307 Query: 316 VADYLASHPKVSSVTFPGLQSGEARRRADAYLKGGYGGLIGFELAGGEEAGRRFIEALRL 375 VA+YL P+VS+V +P LQ+G AR RAD YL GGYGGL+GFEL GG E+GR+FI+ L L Sbjct: 308 VANYLLKKPEVSTVIYPSLQTGAARERADKYLVGGYGGLVGFELRGGAESGRKFIDHLEL 367 Query: 376 FYHVFNIGDARSLAIHPATTTHSQLSPEDQRATGVTPGFVRLSIGIEHPDDIIGDIAQAL 435 FYHV NIGD+RSLAIHPATTTHSQL+PE+Q ATGV+ +VRLS+GIEH DDI+ D+ Q+L Sbjct: 368 FYHVANIGDSRSLAIHPATTTHSQLTPEEQLATGVSESYVRLSVGIEHIDDILADLDQSL 427 Lambda K H 0.319 0.136 0.402 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: 612 Number of extensions: 21 Number of successful extensions: 1 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: 438 Length of database: 437 Length adjustment: 32 Effective length of query: 406 Effective length of database: 405 Effective search space: 164430 Effective search space used: 164430 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 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