Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate Ac3H11_2928 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Query= BRENDA::L7N4M1 (449 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2928 Length = 436 Score = 447 bits (1150), Expect = e-130 Identities = 220/429 (51%), Positives = 298/429 (69%), Gaps = 6/429 (1%) Query: 18 FETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTRIGNPTTDV 77 F+T +HAG PDP T ARA PI+ TTS+ F+ + HAA+LF LE G++Y+RI NPT V Sbjct: 9 FDTLALHAGASPDPATGARATPIHLTTSFVFESSDHAASLFNLERGGHVYSRISNPTNAV 68 Query: 78 VEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAKLG 137 +EQR+AALEGGV A+ +SGQAA AI + GAG HIV+S LYGG+ NL HY+L++ G Sbjct: 69 LEQRVAALEGGVGAIATASGQAALHLAIATIMGAGSHIVASTALYGGSQNLLHYTLSRFG 128 Query: 138 IEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNGVPLIVDNT 197 IE +FV P D+D W+AAVRPNTK FF ET+ NP +D+LD P VS +AH GVPL+VD+T Sbjct: 129 IETTFVK-PGDIDAWRAAVRPNTKLFFGETVGNPGLDVLDIPTVSSIAHEAGVPLLVDST 187 Query: 198 IATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDW----TQGRFPGFTTPD 253 + +P+LI+P GAD+V HSATK+L GHG + G++VDGG+FDW + G+F T P Sbjct: 188 LTSPWLIKPFEHGADLVYHSATKFLSGHGTVVGGIVVDGGSFDWDGPKSAGKFAELTQPY 247 Query: 254 PSYHGVVFAELGPP-AFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQ 312 +H +VF E AF L+AR + LRD+G+ SP A+L+ QG+ETL LR+ +H+ N + Sbjct: 248 DGFHNMVFTEESTVGAFLLRARREGLRDFGACMSPHTAWLILQGIETLPLRMAQHMRNTE 307 Query: 313 RVAEFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAFVNALK 372 +V EFLAA+ V V + L S P H A++L P+G G+V SF+L G E GK F+ LK Sbjct: 308 KVVEFLAAQPFVSRVGHPMLESHPSHALAQKLLPRGAGSVFSFDLKGNREQGKKFIETLK 367 Query: 373 LHSHVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILADLELG 432 + SH+AN+GD RSLVIHPASTTH ++S G++ G +RL++G+E DD++ DL+ Sbjct: 368 VFSHLANVGDCRSLVIHPASTTHFRMSDEALAGAGITQGTIRLSIGLEDADDLIDDLKRA 427 Query: 433 FAAARRFSA 441 AA + A Sbjct: 428 LKAAEKAGA 436 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: 603 Number of extensions: 25 Number of successful extensions: 4 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: 436 Length adjustment: 32 Effective length of query: 417 Effective length of database: 404 Effective search space: 168468 Effective search space used: 168468 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 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