Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate Dsui_3018 Dsui_3018 OAH/OAS sulfhydrylase
Query= BRENDA::L7N4M1 (449 letters) >FitnessBrowser__PS:Dsui_3018 Length = 433 Score = 455 bits (1171), Expect = e-132 Identities = 225/428 (52%), Positives = 303/428 (70%), Gaps = 3/428 (0%) Query: 16 WSFETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTRIGNPTT 75 ++ +T +HAGQ PDP ARA PIY +TS+ F D+ AAALF +E G++Y+RI NPT Sbjct: 7 YTLDTLALHAGQVPDPQYGARATPIYLSTSFVFKDSDQAAALFNMERAGHVYSRISNPTV 66 Query: 76 DVVEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAK 135 V+E+RIAALEGGV A+ +SGQAA A+ L GAG HIV+S LYGG++NL Y+L + Sbjct: 67 SVLEERIAALEGGVGAIATASGQAAMHLAVATLMGAGSHIVASGALYGGSHNLLDYTLRR 126 Query: 136 LGIEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNGVPLIVD 195 GIE +FV D +D W+AA+RPNT+ F ET+ NP +D+LD P ++ +AH +G+PL+VD Sbjct: 127 FGIETTFVPTRD-VDAWRAAIRPNTRLLFGETLGNPGLDVLDIPRIAALAHEHGLPLLVD 185 Query: 196 NTIATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDW-TQGRFPGFTTPDP 254 +T +PYL++P GAD+V HSATK+L GHG A+ GV+VD GNFDW G+FP T P Sbjct: 186 STFTSPYLLKPFEHGADLVFHSATKFLCGHGTAVGGVLVDSGNFDWEASGKFPTLTEPYD 245 Query: 255 SYHGVVFAELGP-PAFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQR 313 +HG+ FAE AF L+AR + LRD+G+ SP NAF + QG+ETL LR++RHV NA++ Sbjct: 246 GFHGMDFAEESTVAAFLLRARREGLRDFGACMSPMNAFQILQGVETLPLRMQRHVENARK 305 Query: 314 VAEFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAFVNALKL 373 + +FLAA + V SV Y GL S P H A++L P+G G+V SF + GG AGK F+ LKL Sbjct: 306 LVDFLAAHEAVESVAYPGLESHPDHALAQKLLPRGCGSVFSFSVKGGRPAGKKFIETLKL 365 Query: 374 HSHVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILADLELGF 433 SH+AN+GD +SLVIHPASTTH ++S LA G+ G +RL+VG+E DD++ DL G Sbjct: 366 FSHLANVGDAKSLVIHPASTTHFRMSDEALLAAGIGAGTIRLSVGLEDADDLIEDLSRGL 425 Query: 434 AAARRFSA 441 AAA + +A Sbjct: 426 AAAAKAAA 433 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: 560 Number of extensions: 25 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: 449 Length of database: 433 Length adjustment: 32 Effective length of query: 417 Effective length of database: 401 Effective search space: 167217 Effective search space used: 167217 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