Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate SMc02595 SMc02595 cystathionine gamma-synthase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Smeli:SMc02595 Length = 408 Score = 305 bits (781), Expect = 2e-87 Identities = 167/375 (44%), Positives = 228/375 (60%), Gaps = 3/375 (0%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEG 78 T A HG + DP+ G+V+PP+Y +STY + + ++Y R+ NPTR + +A LEG Sbjct: 34 TAAAHG-VATDPAFGSVVPPLYLSSTYEFAGFDTPRAYDYGRSGNPTRDLLAQALAKLEG 92 Query: 79 GTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTD 138 G A SGMAA ++ L V+A D YGGT RL + R L F D D Sbjct: 93 GADAVVTPSGMAALDLLLGRLRRNHLVLAPHDCYGGTLRLL-KARADLGHLTFRLTDQRD 151 Query: 139 PAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLS 198 F+AA+ +V IE+P+NP++++ DIA ++ +A+ G VDNTF SP LQ+PLS Sbjct: 152 FGGFEAALSDAPALVLIESPSNPLMRVTDIARLSTLAKAAGSAVAVDNTFLSPALQQPLS 211 Query: 199 LGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGL 258 LGAD +HSATK+LNGHSD++ G AV+ + A + N G V PFD++L LRGL Sbjct: 212 LGADYAIHSATKFLNGHSDVIAG-AVIAAEPQEAHDLKRWANVTGAVAAPFDAWLTLRGL 270 Query: 259 KTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLK 318 +TL RM + +A+ +A++L+ HPA+ V Y GL H H +A+RQ GFG ++S L+ Sbjct: 271 RTLFARMSSQERSAMTIAEYLDAHPAVRHVHYAGLPDHADHEVARRQQRGFGAMMSFELE 330 Query: 319 GGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVG 378 GG A +RF FTLAESLGGVESLV HPA MTH + RE+ GI D L+RLS+G Sbjct: 331 GGVPAVRRFLAHIRCFTLAESLGGVESLVAHPATMTHLDMGPEARERAGIRDELLRLSIG 390 Query: 379 IEDLGDLRGDLERAL 393 +E + DL LE L Sbjct: 391 LEHIDDLMEGLELGL 405 Lambda K H 0.320 0.134 0.391 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: 490 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 397 Length of database: 408 Length adjustment: 31 Effective length of query: 366 Effective length of database: 377 Effective search space: 137982 Effective search space used: 137982 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 (21.8 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