Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate CA265_RS08190 CA265_RS08190 cystathionine gamma-synthase
Query= SwissProt::P9WGB7 (388 letters) >FitnessBrowser__Pedo557:CA265_RS08190 Length = 371 Score = 320 bits (820), Expect = 4e-92 Identities = 172/376 (45%), Positives = 236/376 (62%), Gaps = 8/376 (2%) Query: 14 PATRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRGGFEYARTGNPTRAALEASLAA 73 P T AIHA TG V P+ S+TF +D GG GG Y+R NP R+ALE ++A Sbjct: 3 PETLAIHASNLVKSITGDVTPPLNLSTTFFRDAEGGYPGGHMYSRVSNPNRSALENTVAK 62 Query: 74 VEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRWDVQYTPVR 133 +E G A AFSSG +A L+PG H++ PDD Y G + + +F +++ + Sbjct: 63 LEYGEDAAAFSSGNTCGLVLFQA-LKPGSHIIAPDDMYWGIKKQLLTIFND-SLEFDFID 120 Query: 134 LADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSAKVLVDNTFASPALQQ 193 DLD + A+I T+LIW+ETP+NPLL + DI IA++ ++ + D+TFASP LQ Sbjct: 121 QTDLDLIQASIRSNTKLIWIETPSNPLLKVTDIEEIAKIAKAKNITLACDSTFASPILQN 180 Query: 194 PLRLGADVVLHSTTKYIGGHSDVVGGALVT-NDEELDEEFAFLQNGAGAVPGPFDAYLTM 252 P+ LGAD+V+HS+TKY+GGHSDV+GG LVT +EL E+ +Q GAVP PFD +L Sbjct: 181 PILLGADIVMHSSTKYLGGHSDVLGGILVTAKKDELWEKIKNIQQTGGAVPSPFDCFLLT 240 Query: 253 RGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAARQMRGFGGMVSV 312 R +KTL RM+ H EN +A++L HP+V +V YPGL SHP H+IA +QM+ FGGM+S Sbjct: 241 RSIKTLAYRMKGHCENGKIIADYLNAHPNVEAVFYPGLESHPQHDIAKKQMKDFGGMMSF 300 Query: 313 RMRAGRRAAQDLCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQLEVPDDLVRLSVG 372 ++ AA + K ++F A SLGGVESLIEH S G + P +L+R+SVG Sbjct: 301 LVKGDVEAAHKVVNKVQLFAQATSLGGVESLIEH-----RYSVEGPDSKTPKNLLRISVG 355 Query: 373 IEDIADLLGDLEQALG 388 +E D++ DL QALG Sbjct: 356 LEHADDIIADLAQALG 371 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: 443 Number of extensions: 20 Number of successful extensions: 5 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: 371 Length adjustment: 30 Effective length of query: 358 Effective length of database: 341 Effective search space: 122078 Effective search space used: 122078 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