Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate WP_012384593.1 BIND_RS08130 cystathionine beta-lyase
Query= SwissProt::P9WGB7 (388 letters) >NCBI__GCF_000019845.1:WP_012384593.1 Length = 395 Score = 191 bits (485), Expect = 3e-53 Identities = 125/386 (32%), Positives = 186/386 (48%), Gaps = 14/386 (3%) Query: 5 RTGHQGISGPATRAIHAGYRPDPATGAVNVPIYASSTFAQ---DGVGGLRGGFEYARTGN 61 R GH+G TR +HAG P G VN PIY ST D + RG F Y G Sbjct: 6 RDGHKGFKS-RTRLVHAGRDPSEQFGYVNTPIYRGSTVLYPTLDDLYARRGRFSYGTQGT 64 Query: 62 PTRAALEASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKV 121 PT ALE + + A +G+AA AL ++ GDH+++ D AY D V Sbjct: 65 PTTQALETAWTELAGAAGTVLVPTGLAAITLALLTAVKAGDHILVTDSAYRPCRNFCDTV 124 Query: 122 FTRWDVQ---YTPVRLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSA 178 R V+ Y P+ L+++ + TR++++ETP + + D+ AI + Sbjct: 125 LRRMGVETTYYDPLIGGGLESL---VRQNTRVVFLETPGSQSFELQDVVAIKAVAEAHDL 181 Query: 179 KVLVDNTFASPALQQPLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDEEFAFLQNG 238 ++DNT+ +P P G D+ + + TKY+ GHSD++ G LV+ + + Sbjct: 182 CTIIDNTWGTPLFFPPHERGMDMAIEAGTKYLSGHSDLLLG-LVSANARWYPRLRATYDA 240 Query: 239 AGAVPGPFDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEI 298 PGP D +L +RGL+T+ LR++ A+A +LA P V VL+P LP PGH + Sbjct: 241 FAMCPGPEDVFLALRGLRTMELRLREAERQGLAMARWLAARPEVVQVLHPALPQCPGHAL 300 Query: 299 AARQMRGFGGMVSVRMRA-GRRAAQDLCAKTRVFILAESLGGVESLIEHPSAMTHASTAG 357 R G G+ SV + R A + +F + S GG ESL+ T+ + Sbjct: 301 WKRDFLGSTGLFSVLLAPFSREALAAMLDGLELFGMGYSWGGFESLVIPFDCRTYRT--A 358 Query: 358 SQLEVPDDLVRLSVGIEDIADLLGDL 383 +Q P +R S+G+EDI DL DL Sbjct: 359 TQWNPPGPALRFSIGLEDIEDLQADL 384 Lambda K H 0.319 0.135 0.393 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: 403 Number of extensions: 24 Number of successful extensions: 6 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: 388 Length of database: 395 Length adjustment: 31 Effective length of query: 357 Effective length of database: 364 Effective search space: 129948 Effective search space used: 129948 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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