Align cystathionine β-synthase (O-acetyl-L-serine) monomer (EC 4.2.1.22; EC 2.5.1.134; EC 2.5.1.47) (characterized)
to candidate Ga0059261_3644 Ga0059261_3644 cysteine synthase A
Query= metacyc::HP_RS00545-MONOMER (306 letters) >FitnessBrowser__Korea:Ga0059261_3644 Length = 306 Score = 208 bits (530), Expect = 1e-58 Identities = 116/298 (38%), Positives = 171/298 (57%), Gaps = 6/298 (2%) Query: 6 TMQDAIGRTPVFKFTNKDYPIPLNSAIYAKLEHLNPGGSVKDRLGQYLIGEGFKTGKITS 65 T+ + IG TP + + +P + ++ K E NPGGS+KDR+ ++ G + Sbjct: 5 TILETIGNTPHIRI-QRLFP---GAEVWVKSERSNPGGSIKDRIALSMVEAAEADGSLKP 60 Query: 66 KTTIIEPTAGNTGIALALVAIKHHLKTIFVVPEKFSTEKQQIMRALGALVINTPTSEGIS 125 TI+EPT+GNTG+ LA+VA K I V+PE S E++++M A GA TP +G+ Sbjct: 61 GGTIVEPTSGNTGVGLAMVAAVKGYKLILVMPESMSIERRRLMLAYGATFDLTPREKGMK 120 Query: 126 GAIKKSKELAESIPDSYLPLQFENPDNPAAYYHTLAPEIVQELG-TNLTSFVAGIGSGGT 184 GAI+++ E+ ES P +++P QFENP N + T A EI+ + + + G+G+GG Sbjct: 121 GAIERAVEIVESTPGAWMPQQFENPANVDVHVKTTAQEILNDFADAPVDVIITGVGTGGH 180 Query: 185 FAGTARYLKERIPAIRLIGVEPEGS-ILNGGEPGPHEIEGIGVEFIPPFFENLDIDGFET 243 G A LK+ P +++ VEPE S +++GG+PGPH I+GIG F+P IDG Sbjct: 181 ITGVAETLKKSWPNLKVYAVEPELSPVISGGQPGPHPIQGIGAGFVPKNLHTDAIDGAIQ 240 Query: 244 ISDEEGFSYTRKLAKKNGLLVGSSSGAAFVAALKEAQRLPEGSQVLTIFPDVADRYLS 301 + Y R+ A++ GLLVG SSGA A K+ LP GS+VL D +RYLS Sbjct: 241 VDAGNAKDYARRAAREEGLLVGISSGATLAAIAKKLPDLPAGSRVLGFNYDTGERYLS 298 Lambda K H 0.316 0.137 0.389 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: 268 Number of extensions: 15 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: 306 Length of database: 306 Length adjustment: 27 Effective length of query: 279 Effective length of database: 279 Effective search space: 77841 Effective search space used: 77841 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 (21.6 bits) S2: 48 (23.1 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