Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate BPHYT_RS09190 BPHYT_RS09190 cystathionine beta-lyase
Query= SwissProt::P9WGB7 (388 letters) >FitnessBrowser__BFirm:BPHYT_RS09190 Length = 394 Score = 159 bits (402), Expect = 1e-43 Identities = 119/387 (30%), Positives = 180/387 (46%), Gaps = 23/387 (5%) Query: 16 TRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRG-------GFEYARTGNPTRAALE 68 TR + A + P + ++P+ +ST + +R + Y PT AL Sbjct: 12 TRIVRAEDQLTPGFESFSMPVTRASTVVFPDLATMRALDWKNDAQWRYGLHATPTSLALA 71 Query: 69 ASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRWDVQ 128 LA +E G A SG+++ +++ GD V+IPD+ Y D + + + Sbjct: 72 QRLATIEGGNHALLQPSGLSSISNVYFGLVKAGDDVLIPDNVYSPNRDHGDWLARDFGIT 131 Query: 129 ---YTPV---RLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSAKVLV 182 Y P+ +ADL I P TRLIW+E P + + +AD+ AI R+ + Sbjct: 132 VRYYDPMIGAGMADL------IQPNTRLIWLEAPGSVTMEVADVPAITAAARARNVVTAI 185 Query: 183 DNTFASPALQQPLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDEEFAFLQNGAGAV 242 DNT+++ +P G D+ + + TKY G DV+ GA +T D EL + + G Sbjct: 186 DNTWSAGLGFRPFDHGVDISVQALTKYQSGGGDVLMGATITVDRELHLKLKAARMRMGIG 245 Query: 243 PGPFDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAARQ 302 D L +R L T+ LR ++H +A +A++L P +++VL+P L PGHE R Sbjct: 246 VSSDDCSLILRSLPTMQLRFEQHDRSALGLAKWLKTRPEIAAVLHPALSDCPGHEFYKRD 305 Query: 303 MRGFGGMVSVRMRAGRRAAQ--DLCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQL 360 G GG+ SV AQ C +F L S GG SL P + TAG Q Sbjct: 306 FTGAGGLFSVVFDGRYSPAQIDTFCESLELFSLGWSWGGAHSL-AMPYDVASMRTAG-QW 363 Query: 361 EVPDDLVRLSVGIEDIADLLGDLEQAL 387 LVR +G+E ADL D+EQ+L Sbjct: 364 PHSGTLVRFYIGLEAEADLRADMEQSL 390 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: 401 Number of extensions: 23 Number of successful extensions: 3 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: 394 Length adjustment: 31 Effective length of query: 357 Effective length of database: 363 Effective search space: 129591 Effective search space used: 129591 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