Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate YP_425865.1 Rru_A0774 O-acetylhomoserine/O-acetylserine sulfhydrylase
Query= metacyc::MONOMER-17873 (438 letters) >NCBI__GCF_000013085.1:YP_425865.1 Length = 438 Score = 870 bits (2249), Expect = 0.0 Identities = 438/438 (100%), Positives = 438/438 (100%) Query: 1 MTVDVAPPKAAQYHQDTLALHGGSYRADPTTGAVAVPIYQTTSYQVHDTAHAARLAGLEE 60 MTVDVAPPKAAQYHQDTLALHGGSYRADPTTGAVAVPIYQTTSYQVHDTAHAARLAGLEE Sbjct: 1 MTVDVAPPKAAQYHQDTLALHGGSYRADPTTGAVAVPIYQTTSYQVHDTAHAARLAGLEE 60 Query: 61 IGFAYTRIGNPTQDAFEQRLAALEGGVAALALASGQAASAIAVLTLAQAGDNIVTSTDLY 120 IGFAYTRIGNPTQDAFEQRLAALEGGVAALALASGQAASAIAVLTLAQAGDNIVTSTDLY Sbjct: 61 IGFAYTRIGNPTQDAFEQRLAALEGGVAALALASGQAASAIAVLTLAQAGDNIVTSTDLY 120 Query: 121 GGTWNLFANTLRTLGIEARFVDPADPEAFRRATDARTRLYYGETLPNPKLTVFPIAEVAA 180 GGTWNLFANTLRTLGIEARFVDPADPEAFRRATDARTRLYYGETLPNPKLTVFPIAEVAA Sbjct: 121 GGTWNLFANTLRTLGIEARFVDPADPEAFRRATDARTRLYYGETLPNPKLTVFPIAEVAA 180 Query: 181 IGRSLGVPLIIDNTATPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGAIIDGGTFPWADH 240 IGRSLGVPLIIDNTATPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGAIIDGGTFPWADH Sbjct: 181 IGRSLGVPLIIDNTATPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGAIIDGGTFPWADH 240 Query: 241 AERHALLTGPEPSYHNASWTDLAAPFGPLAYILRARAGVLRDLGASIAPVSAFNLIQGLE 300 AERHALLTGPEPSYHNASWTDLAAPFGPLAYILRARAGVLRDLGASIAPVSAFNLIQGLE Sbjct: 241 AERHALLTGPEPSYHNASWTDLAAPFGPLAYILRARAGVLRDLGASIAPVSAFNLIQGLE 300 Query: 301 TLPLRLARHNANAIKVADYLASHPKVSSVTFPGLQSGEARRRADAYLKGGYGGLIGFELA 360 TLPLRLARHNANAIKVADYLASHPKVSSVTFPGLQSGEARRRADAYLKGGYGGLIGFELA Sbjct: 301 TLPLRLARHNANAIKVADYLASHPKVSSVTFPGLQSGEARRRADAYLKGGYGGLIGFELA 360 Query: 361 GGEEAGRRFIEALRLFYHVFNIGDARSLAIHPATTTHSQLSPEDQRATGVTPGFVRLSIG 420 GGEEAGRRFIEALRLFYHVFNIGDARSLAIHPATTTHSQLSPEDQRATGVTPGFVRLSIG Sbjct: 361 GGEEAGRRFIEALRLFYHVFNIGDARSLAIHPATTTHSQLSPEDQRATGVTPGFVRLSIG 420 Query: 421 IEHPDDIIGDIAQALDLV 438 IEHPDDIIGDIAQALDLV Sbjct: 421 IEHPDDIIGDIAQALDLV 438 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: 850 Number of extensions: 20 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: 438 Length adjustment: 32 Effective length of query: 406 Effective length of database: 406 Effective search space: 164836 Effective search space used: 164836 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