Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate Ac3H11_4146 Cystathionine beta-lyase (EC 4.4.1.8)
Query= SwissProt::P9WGB7 (388 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4146 Length = 412 Score = 168 bits (426), Expect = 2e-46 Identities = 126/398 (31%), Positives = 182/398 (45%), Gaps = 29/398 (7%) Query: 15 ATRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRG-------GFEYARTGNPTRAAL 67 ATR +H GY P A +Y +ST V +R G+ Y G PT L Sbjct: 12 ATRIVHHGYLPPAGFEAPQPGVYKASTVIFPNVAAMRSREWKDKSGYTYGLHGTPTTFIL 71 Query: 68 EASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRWDV 127 E L +E G SG+AA A+L+PGD V+IPD+AYG + R+ + Sbjct: 72 EERLCTLEGGLQCVLVPSGLAAIANVGLALLKPGDEVLIPDNAYGPGKDFANGELARFGI 131 Query: 128 Q---YTPVRLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSAKVLVDN 184 Y P+ ADL A ITP TRL+W+E P + + D+ + R +DN Sbjct: 132 THVFYDPLDPADL---AARITPATRLVWLEAPGSVSMEFPDLCEQVRICRARGVTTALDN 188 Query: 185 TFASPALQQPL------RLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDEEFAFLQNG 238 T+ + P LG D+ H+ TKY G DV+ G+++T D L + Sbjct: 189 TWGAGLAFAPFDLTGDGSLGVDISAHALTKYPSGGGDVLMGSVITRDLGLHMKIKLTHMR 248 Query: 239 AGAVPGPFDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGH-- 296 G G D +R L ++ LR + H E A +A +L P+++ VL+P L PGH Sbjct: 249 LGLGVGVNDVEAVLRALPSIGLRYRAHDEAARVLARWLQQQPAIAQVLHPALEGAPGHAH 308 Query: 297 --EIAARQMRGFG---GMVSVRM--RAGRRAAQDLCAKTRVFILAESLGGVESLIEHPSA 349 + G G G+ SV + R ++ C R+F L S GG SL+ + Sbjct: 309 WKALCGAAQGGQGAAAGLFSVMIDARYTQQQVDAFCDGLRLFKLGYSWGGPMSLVVPYTI 368 Query: 350 MTHASTAGSQLEVPDDLVRLSVGIEDIADLLGDLEQAL 387 + S QL+ P LVR S+G+E + DL DL+QA+ Sbjct: 369 GSMRSRPSPQLQ-PGTLVRFSIGLEAVEDLQRDLQQAM 405 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: 444 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: 412 Length adjustment: 31 Effective length of query: 357 Effective length of database: 381 Effective search space: 136017 Effective search space used: 136017 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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