Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate N515DRAFT_4305 N515DRAFT_4305 cystathionine gamma-lyase
Query= SwissProt::O31631 (373 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_4305 N515DRAFT_4305 cystathionine gamma-lyase Length = 392 Score = 310 bits (795), Expect = 3e-89 Identities = 160/368 (43%), Positives = 226/368 (61%), Gaps = 18/368 (4%) Query: 13 GNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLENGARGLA 72 G D TG + PIY ++ Y G+ G++Y RT+NPTR E +A LE G G A Sbjct: 24 GQSPDPTTGAIMTPIYATSTYVQESPGKHKGYEYSRTQNPTRMAYEACVAALEGGVAGFA 83 Query: 73 FSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKY-GLTFHYDDFSDEDCLRS 131 F SG+AA T++ L SG +I DLYGG+YRLFE ++ GL F + D +D L++ Sbjct: 84 FGSGLAAAATVLDLLDSGSHVIAMDDLYGGSYRLFERVRRRSAGLDFTFVDLNDAQALKA 143 Query: 132 KITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLELGADIV 191 + PNTK ++ ETPTNP+++ D+ +A K+HGL+L+VDNTF +P++QRP E GAD+V Sbjct: 144 ALKPNTKMIWAETPTNPMLKLVDLAKVAAFAKKHGLILVVDNTFCSPMIQRPFESGADLV 203 Query: 192 IHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKTLSLRM 251 +HSATKYL GH+D++ G+VV +++ L E M QN++GAV PFDS+L MRG+KTL LRM Sbjct: 204 LHSATKYLNGHSDMVGGIVVAREQELAERMGFLQNSVGAVAGPFDSFLAMRGLKTLHLRM 263 Query: 252 RQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRLQKE-EWVN 294 + H +A ELA +LE+ E+ V+YPG GG++S ++ Sbjct: 264 KAHCESALELAQWLEKHPEVERVIYPGLKSHPQHALARRQMHGFGGIISIEVKGGLRKAR 323 Query: 295 PFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGIEHAEDL 354 L+ AESLGGVES I +PA TH +P R G+ + L+R SVG+E DL Sbjct: 324 RMLERCHLFALAESLGGVESLIEHPAIMTHASVPPANRKRLGISDSLIRLSVGVEDIADL 383 Query: 355 KEDLKQAL 362 + +L +AL Sbjct: 384 RSELAEAL 391 Lambda K H 0.319 0.135 0.392 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: 361 Number of extensions: 10 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: 373 Length of database: 392 Length adjustment: 30 Effective length of query: 343 Effective length of database: 362 Effective search space: 124166 Effective search space used: 124166 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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