Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate Ga0059261_1458 Ga0059261_1458 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= SwissProt::P9WGB7 (388 letters) >FitnessBrowser__Korea:Ga0059261_1458 Length = 440 Score = 216 bits (551), Expect = 8e-61 Identities = 150/403 (37%), Positives = 214/403 (53%), Gaps = 30/403 (7%) Query: 14 PATRAIHAGYRPDPATGAVNVPIYASSTFAQ----------DGVGGLR-GGFE---YART 59 PAT + GY P + G++ PI+A+STF +GV G R GG E Y+R Sbjct: 36 PATLMMGHGYDPMLSEGSLKPPIFATSTFVFPNAAAGKRHFEGVTGKRPGGAEGLVYSRF 95 Query: 60 GNPTRAALEASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLID 119 P + LE L EE A AFSSGM+A AM++PGD +V Y T LI Sbjct: 96 NGPNQEILEDRLGIWEEAEDALAFSSGMSAIATLFLAMVKPGDTIVHSGPLYAATETLIA 155 Query: 120 KVFTRWDVQYTPVRLA----DLDAV-GAAITPRTRLIWVETPTNPLLSIADITAIAE--- 171 ++ ++ V + ++DAV A + LI++E+P NP ++ D+ A+A Sbjct: 156 RILGKFGVHWLDFPAGATREEIDAVLSKAASGNVALIYLESPANPTNALVDVEAVAASRD 215 Query: 172 -LGTDRSAK-VLVDNTFASPALQQPLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELD 229 + T S + +DNTF P +PL+ GAD+V++S TKY GGHSD+V G V +EL Sbjct: 216 AIFTGASKPPIAIDNTFLGPLWAKPLQQGADLVVYSLTKYAGGHSDLVAGG-VLGSKELI 274 Query: 230 EEFAFLQNGAGAVPGPFDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPG 289 ++N G + P A++ +R L+TL LRM R ENA V E+L HP V SV Y G Sbjct: 275 NTIRLMRNTIGTICDPNTAWMLLRSLETLELRMSRAGENAIKVCEYLRTHPKVESVGYLG 334 Query: 290 -LP-SHPGHEIAARQMRGFGGMVSVRMRAGRRAAQDLCAKTRVFILAESLGGVESLIEHP 347 LP +I R G G S+ ++ G + A ++ LA SLGG E+L P Sbjct: 335 FLPEGSRQRDIYDRHCTGAGSTFSLYLKGGEKEAFAFLDSLKIAKLAVSLGGTETLASAP 394 Query: 348 SAMTHASTAGSQ---LEVPDDLVRLSVGIEDIADLLGDLEQAL 387 +AMTH S ++ L + D+LVR+S+G+ED DL+ D E+AL Sbjct: 395 AAMTHLSVPDARKKALGITDNLVRISIGVEDADDLIADFEEAL 437 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: 445 Number of extensions: 26 Number of successful extensions: 7 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: 440 Length adjustment: 31 Effective length of query: 357 Effective length of database: 409 Effective search space: 146013 Effective search space used: 146013 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