Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate PP_4594 PP_4594 putative Cystathionine gamma-synthase
Query= SwissProt::P9WGB7 (388 letters) >FitnessBrowser__Putida:PP_4594 Length = 393 Score = 310 bits (795), Expect = 3e-89 Identities = 173/378 (45%), Positives = 238/378 (62%), Gaps = 8/378 (2%) Query: 15 ATRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRGGFEYARTGNPTRAALEASLAAV 74 ATR IHAG + A A+ I +S+F + + + + Y+R GNPTR A E +AA+ Sbjct: 13 ATRTIHAGEQFSVADNAIFPAIVTASSFTKRSLDD-KPEYSYSRVGNPTRHAYETCVAAL 71 Query: 75 EEGAFARAFSSGMAATDCALRAMLRPGD-HVVIPDDAYGGTFRLIDKVFTRWD-VQYTPV 132 EEG A A +SG+ AT L L P D HVV+ + YGGTFR+++ +R + T V Sbjct: 72 EEGVGAVACASGVNATATVLE--LLPKDAHVVVMNGVYGGTFRIMEDYRSRTSGLTTTYV 129 Query: 133 RLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSAKVLVDNTFASPALQ 192 L D++AV AAI P T+LIW+E+PTNPLL + DI A+ +L + +DNTF SP Q Sbjct: 130 DLNDIEAVAAAIKPETQLIWIESPTNPLLHLVDIKAVCDLAKAKGILTCIDNTFCSPWNQ 189 Query: 193 QPLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDEEFAFLQNGAGAVPGPFDAYLTM 252 +P+ LG D+V+HS +KYIGGHSD+ GG +V ++ L + GAV GPFD YL + Sbjct: 190 RPITLGVDLVMHSASKYIGGHSDLTGGVVVAANDALLARLRRISMAIGAVQGPFDCYLAL 249 Query: 253 RGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAARQMRGFGGMVSV 312 RGLKTL +RM+R NA VA FL H V V YPGL SHP HE+ RQMR G +V++ Sbjct: 250 RGLKTLDVRMERQCANALQVARFLEGHAQVEQVYYPGLESHPQHELCKRQMRSGGAVVAM 309 Query: 313 RMRAGRRAAQDLCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQ---LEVPDDLVRL 369 +++ R A L ++F+LA+SLGGVES+I H +M+H S + Q + + ++L+RL Sbjct: 310 KVKGDRAALNRLVEALQIFVLADSLGGVESMINHSWSMSHCSLSPEQKGVMGISENLLRL 369 Query: 370 SVGIEDIADLLGDLEQAL 387 SVGIED DL+ DL+ AL Sbjct: 370 SVGIEDYRDLVEDLDGAL 387 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: 427 Number of extensions: 17 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: 393 Length adjustment: 31 Effective length of query: 357 Effective length of database: 362 Effective search space: 129234 Effective search space used: 129234 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