Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Dsui_0429 Dsui_0429 cystathionine beta-lyase/cystathionine gamma-synthase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__PS:Dsui_0429 Length = 382 Score = 236 bits (603), Expect = 6e-67 Identities = 148/382 (38%), Positives = 209/382 (54%), Gaps = 13/382 (3%) Query: 14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFE-YSRTHNPTRFAYERC 72 +L+ T A G D + ++PP++ +T+ ++ G + G YSR +P E Sbjct: 9 SLAPETQAARGTVPVDSTYRDIVPPLHLATTFERAGDGSYPGGRVYSRDGSPAYDGPEAL 68 Query: 73 VAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFS 132 + LEGG A FASGMAA S V++ L G+ VVA +Y + L + + A + Sbjct: 69 LKELEGGAAAALFASGMAAASAVLQALKPGARVVAPRAMY---WALRNWMIQFAANWQLT 125 Query: 133 FVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPM 192 D A A ++ +VW+ETP NP ++ DIAA A A G VVD+T +P+ Sbjct: 126 LEFFADDAELAALLQRPADLVWLETPANPTWEITDIAAAAKAAHAAGARLVVDSTVPTPV 185 Query: 193 LQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSF 252 RPL LGAD+V+HSATKYLNGHSD+V G V + +++ ++ G V GPF+++ Sbjct: 186 FTRPLELGADVVMHSATKYLNGHSDVVAGALVTRTEDDFWQRIKTVRALGGAVLGPFEAW 245 Query: 253 LALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQM-SGFGG 311 L RG++TL R+R +A A+A H + V+YPGL SHP H +A RQM GFG Sbjct: 246 LLARGMRTLFPRVRTAAASAAAIASHFHGHAKVGLVLYPGLPSHPGHAVAARQMQGGFGA 305 Query: 312 IVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDA 371 ++S+ + GG AAK + ++F A SLG VESLV H A + D Sbjct: 306 MLSLRIAGGEAAAKAVAARLQVFQRATSLGSVESLVEHRASVEGPG--------TFCPDD 357 Query: 372 LVRLSVGIEDLGDLRGDLERAL 393 L+RLSVGIE DL DLE+AL Sbjct: 358 LLRLSVGIEATADLIADLEQAL 379 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: 399 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: 397 Length of database: 382 Length adjustment: 30 Effective length of query: 367 Effective length of database: 352 Effective search space: 129184 Effective search space used: 129184 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