Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate N515DRAFT_4305 N515DRAFT_4305 cystathionine gamma-lyase
Query= BRENDA::Q1M0P5 (380 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_4305 N515DRAFT_4305 cystathionine gamma-lyase Length = 392 Score = 400 bits (1029), Expect = e-116 Identities = 201/373 (53%), Positives = 261/373 (69%), Gaps = 2/373 (0%) Query: 5 TKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIADLEG 64 T IH G S D TTGA+ PIY TSTY Q++ G HKGYEYSR+ NPTR A E +A LEG Sbjct: 18 TLAIHAGQSPDPTTGAIMTPIYATSTYVQESPGKHKGYEYSRTQNPTRMAYEACVAALEG 77 Query: 65 GVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKN-GLSCTIIDTSD 123 GV GFAF SGLA V LL SG HV+ DD+YGG++RLF +V ++ GL T +D +D Sbjct: 78 GVAGFAFGSGLAAAATVLDLLDSGSHVIAMDDLYGGSYRLFERVRRRSAGLDFTFVDLND 137 Query: 124 LSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPLL 183 +K A+KPNTK ++ ETP+NP+LK+ DLA+ A+ AK HGL+ +VDNTF +P Q P Sbjct: 138 AQALKAALKPNTKMIWAETPTNPMLKLVDLAKVAAFAKKHGLILVVDNTFCSPMIQRPFE 197 Query: 184 LGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQRGIK 243 GAD+V+HS TKYL GHSD+V G+V + LA+ + F QN++G V GP DS+L RG+K Sbjct: 198 SGADLVLHSATKYLNGHSDMVGGIVVAREQELAERMGFLQNSVGAVAGPFDSFLAMRGLK 257 Query: 244 TLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFTLKN 303 TL LRM+AH ++AL +A++LEKHP+VERV YPGL +HP + LA++QM GF G++S +K Sbjct: 258 TLHLRMKAHCESALELAQWLEKHPEVERVIYPGLKSHPQHALARRQMHGFGGIISIEVKG 317 Query: 304 D-SEATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRLSVGI 362 +A +E LF L ESLGGVESL+ PA MTHA +P R+ GI D L+RLSVG+ Sbjct: 318 GLRKARRMLERCHLFALAESLGGVESLIEHPAIMTHASVPPANRKRLGISDSLIRLSVGV 377 Query: 363 EHEQDLLEDLEQA 375 E DL +L +A Sbjct: 378 EDIADLRSELAEA 390 Lambda K H 0.318 0.136 0.394 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: 453 Number of extensions: 16 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: 380 Length of database: 392 Length adjustment: 30 Effective length of query: 350 Effective length of database: 362 Effective search space: 126700 Effective search space used: 126700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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