Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate WP_013421124.1 RVAN_RS18015 PLP-dependent transferase
Query= SwissProt::P9WGB7 (388 letters) >NCBI__GCF_000166055.1:WP_013421124.1 Length = 382 Score = 283 bits (725), Expect = 4e-81 Identities = 168/377 (44%), Positives = 224/377 (59%), Gaps = 9/377 (2%) Query: 14 PATRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRGGFEYARTGNPTRAALEASLAA 73 P T A A R D ATGA+ P+Y S+T+ +D R G Y+R N T +L A Sbjct: 6 PETVAASALGREDEATGALIPPLYPSTTYIRDPDNLYRRGRVYSRAQNATFDTAAETLTA 65 Query: 74 VEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRWDVQYTPVR 133 +E GA F SGMAA + A L PGDHVV P Y ++ +RW + Sbjct: 66 LEGGAETALFGSGMAAANAVFLA-LAPGDHVVAPRVMYWALRAWLEGFASRWGLLVDFAD 124 Query: 134 LADLDAVGAAITP-RTRLIWVETPTNPLLSIADITAIAELGTDRSAKVLVDNTFASPALQ 192 D+DA+ AAI P RT+L+W+ETP NPL ++ DI A AE+ A++ VD+T A+P L Sbjct: 125 AGDIDALKAAIVPGRTKLVWLETPANPLWTVYDIAATAEIAHAAGARLAVDSTVATPVLT 184 Query: 193 QPLRLGADVVLHSTTKYIGGHSDVVGGALVT-NDEELDEEFAFLQNGAGAVPGPFDAYLT 251 +PL LGAD+V+HS TKY+ GHSD V G + T ++ +Q+ G VPG +A+L Sbjct: 185 RPLSLGADIVMHSATKYLNGHSDAVIGTVTTARQDDFWATIKTVQSQNGGVPGTLEAWLL 244 Query: 252 MRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAARQMR-GFGGMV 310 RG++TL R++ S +A +AE + HP V+ VLYPGLP GHE+A RQM+ GFGGM+ Sbjct: 245 QRGMRTLFPRVRWQSASAQTLAERFSAHPGVAEVLYPGLPGFKGHELAQRQMQGGFGGML 304 Query: 311 SVRMRAGRRAAQDLCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQLEVPDDLVRLS 370 S+R+ G RAA A ++ A SLGGVESLIEH AS G + VP DL+RLS Sbjct: 305 SIRVHGGERAAIATAAHVSIWKRATSLGGVESLIEH-----RASIEGPRSPVPADLLRLS 359 Query: 371 VGIEDIADLLGDLEQAL 387 VG+E + DL DL +AL Sbjct: 360 VGLEAVDDLYDDLSEAL 376 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: 422 Number of extensions: 27 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: 382 Length adjustment: 30 Effective length of query: 358 Effective length of database: 352 Effective search space: 126016 Effective search space used: 126016 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