Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate 3607593 Dshi_1002 Cystathionine gamma-synthase (RefSeq)
Query= SwissProt::P9WGB7 (388 letters) >FitnessBrowser__Dino:3607593 Length = 380 Score = 260 bits (665), Expect = 4e-74 Identities = 165/379 (43%), Positives = 217/379 (57%), Gaps = 11/379 (2%) Query: 14 PATRAIHAGYRPDPATGAVNVPIYASSTFAQD-GVGGLRGGFEYARTGNPTRAALEASLA 72 P T A H G D A+G V PI ++TF + L Y+R + A+E LA Sbjct: 9 PDTLAAHGGGAVDTASGGVVPPIQPATTFRRGPDYAPLNPDNIYSRDDSEALRAVETLLA 68 Query: 73 AVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRWDVQYTPV 132 A+E GA A AF SGMAAT R L G VV+ Y GT + + R V V Sbjct: 69 ALEGGAGALAFPSGMAATAAVFRT-LPAGARVVLQSGIYWGTTKWVRDFCARRGVTLVEV 127 Query: 133 RLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSAKVLVDNTFASPALQ 192 AD A+G+A T L++VETP+NP L DI A A A ++VD+T A+P L Sbjct: 128 DAADAHALGSACAAPTALVFVETPSNPWLKTVDIRAAAAAAHGAGALLVVDSTAATPVLT 187 Query: 193 QPLRLGADVVLHSTTKYIGGHSDVVGGALVTND--EELDEEFAFLQNGAGAVPGPFDAYL 250 +PL LGAD+V+HS TK + GHSDV+ GALVT D E A ++ AGAV GPF+A+L Sbjct: 188 RPLGLGADLVMHSATKGLNGHSDVLAGALVTADAGHETWARIATDRHDAGAVLGPFEAWL 247 Query: 251 TMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAARQMR-GFGGM 309 +RG++TL LR+ R S A +A+ L+ V+ V YPGLP H GH+IA QM GFGG+ Sbjct: 248 LLRGMRTLPLRVARMSATALELAQRLSTDTRVADVFYPGLPGHAGHDIAVAQMTGGFGGL 307 Query: 310 VSVRMRAGRRAAQDLCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQLEVPDDLVRL 369 +S + R+ A ++ + +F A SLGGVESL+E H +T +P+ LVRL Sbjct: 308 MSFLVHGDRQTALEVVGRLELFQRATSLGGVESLVE------HRATIEPDSGIPETLVRL 361 Query: 370 SVGIEDIADLLGDLEQALG 388 SVGIED DL DL++ALG Sbjct: 362 SVGIEDAGDLWADLDRALG 380 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: 457 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: 380 Length adjustment: 30 Effective length of query: 358 Effective length of database: 350 Effective search space: 125300 Effective search space used: 125300 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 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