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 WP_011382646.1 AMB_RS01005 cysteine synthase A
Query= metacyc::HP_RS00545-MONOMER (306 letters) >NCBI__GCF_000009985.1:WP_011382646.1 Length = 319 Score = 226 bits (576), Expect = 5e-64 Identities = 126/306 (41%), Positives = 183/306 (59%), Gaps = 4/306 (1%) Query: 3 IITTMQDAIGRTPVFKFTNKDYPIPLNSAIYAKLEHLNPGGSVKDRLGQYLIGEGFKTGK 62 I ++ D IG TP+ +F + I KLE NP SVKDR+G +I +G+ Sbjct: 12 IYDSIIDTIGATPLVRFKRMAAEAGSKADIVGKLEFFNPLASVKDRIGFAMIEAAEVSGQ 71 Query: 63 ITSKTTIIEPTAGNTGIALALVAIKHHLKTIFVVPEKFSTEKQQIMRALGALVINTPTSE 122 + TIIEPT+GNTGIALA VA K I +PE S E++++++ LGA ++ TP S+ Sbjct: 72 LKPGGTIIEPTSGNTGIALAFVAAAKGYKLILCMPESMSLERRKMLQLLGAEIVLTPASK 131 Query: 123 GISGAIKKSKELAESIPDSYLPLQFENPDNPAAYYHTLAPEIVQELGTNLTSFVAGIGSG 182 G++GA+++++EL S P + +P QF+N NPA + T A EI + + V+G+G+G Sbjct: 132 GMTGAVRQAEELLASTPGAIMPQQFKNEANPAIHERTTAEEIWNDTNGKVDIIVSGVGTG 191 Query: 183 GTFAGTARYLKERIPAIRLIGVEPEGS-ILNGGEPGPHEIEGIGVEFIPPFFENLDIDGF 241 GT +G LK R P ++++ VEPE S +L+GG PGPH+I+GIG F+P + ID Sbjct: 192 GTISGIGHVLKARKPGLKMVAVEPEDSPVLSGGAPGPHKIQGIGAGFVPDILDKGVIDEI 251 Query: 242 ETISDEEGFSYTRKLAKKNGLLVGSSSGAAFVAALKEAQRLPE--GSQVLTIFPDVADRY 299 I +E + RK AK G+ VG SSGAA AAL+ R PE G ++ I P A+RY Sbjct: 252 LQIGNETALATARKAAKLEGVPVGISSGAAIAAALELGSR-PENAGKLIVAIIPSFAERY 310 Query: 300 LSKGIY 305 LS ++ Sbjct: 311 LSTALF 316 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: 244 Number of extensions: 13 Number of successful extensions: 2 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: 319 Length adjustment: 27 Effective length of query: 279 Effective length of database: 292 Effective search space: 81468 Effective search space used: 81468 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