Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_011605484.1 FRAAL_RS19065 bifunctional o-acetylhomoserine/o-acetylserine sulfhydrylase
Query= BRENDA::L7N4M1 (449 letters) >NCBI__GCF_000058485.1:WP_011605484.1 Length = 430 Score = 600 bits (1547), Expect = e-176 Identities = 298/424 (70%), Positives = 350/424 (82%), Gaps = 2/424 (0%) Query: 16 WSFETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTRIGNPTT 75 WSFET+QIHAG PDP T ARA+PIY TTSY F DT HAAALF L PGNIYTRI NPT Sbjct: 6 WSFETQQIHAGAQPDPATGARAVPIYQTTSYVFRDTDHAAALFALGEPGNIYTRIMNPTQ 65 Query: 76 DVVEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAK 135 DV EQRI+ LEGGV AL +SGQAAET AILNLA +GDH+VSS LYGGTYNLFHY+L K Sbjct: 66 DVFEQRISTLEGGVGALATASGQAAETLAILNLAESGDHVVSSSSLYGGTYNLFHYTLPK 125 Query: 136 LGIEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNGVPLIVD 195 LGIEV+FV DPDDL+ W+ AVRPNTKAF+ ETI NP+ D+LDT VSEVAH +G+PLIVD Sbjct: 126 LGIEVTFVADPDDLEQWRDAVRPNTKAFYGETIGNPRGDILDTAGVSEVAHAHGIPLIVD 185 Query: 196 NTIATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDW-TQGRFPGFTTPDP 254 NT+ATPYL +PL GADIVVHSATK++GGHG AI GVIVDGG FD+ GRF FTTPDP Sbjct: 186 NTLATPYLYRPLEHGADIVVHSATKFIGGHGTAIGGVIVDGGRFDFGASGRFANFTTPDP 245 Query: 255 SYHGVVFAE-LGPPAFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQR 313 SYHG+V+ E LG ++ KARVQLLRD G++ SPFN+FL+ QGLETLSLR+ERH ANAQR Sbjct: 246 SYHGLVYWEALGHGSYIAKARVQLLRDIGASISPFNSFLLLQGLETLSLRVERHTANAQR 305 Query: 314 VAEFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAFVNALKL 373 VAE+L ARD+V V Y GLPSS W++RA+R+ P+G GA+LSF +AGG AG+ FV ++L Sbjct: 306 VAEWLEARDEVSWVAYPGLPSSKWYDRAQRVLPRGAGAILSFGIAGGAAAGRKFVEGVEL 365 Query: 374 HSHVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILADLELGF 433 SH+AN+GD RSL+IHPA+TTH+QL+ AEQ ATGV+P L+RL+VGIEGIDDILADL+ GF Sbjct: 366 FSHLANVGDARSLIIHPATTTHSQLTEAEQAATGVTPDLIRLSVGIEGIDDILADLDAGF 425 Query: 434 AAAR 437 AA+ Sbjct: 426 RAAK 429 Lambda K H 0.318 0.134 0.394 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: 664 Number of extensions: 24 Number of successful extensions: 3 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: 449 Length of database: 430 Length adjustment: 32 Effective length of query: 417 Effective length of database: 398 Effective search space: 165966 Effective search space used: 165966 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: 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