Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_081449436.1 RVAN_RS09315 PLP-dependent transferase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000166055.1:WP_081449436.1 Length = 412 Score = 444 bits (1142), Expect = e-129 Identities = 228/382 (59%), Positives = 287/382 (75%), Gaps = 3/382 (0%) Query: 13 RALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERC 72 R AT +H G D +TGAVM PIYA+ST+AQSSPG+H G+EY+R+ NPTR A+E+ Sbjct: 30 RHTKTATKVVHAGVEHD-ATGAVMTPIYASSTFAQSSPGKHTGWEYARSGNPTRAAFEKA 88 Query: 73 VAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFS 132 VA LEGG FAFASGMAA +TV+ELLD GSH+VA DDLYGGT+RL ERVR+RTAG + Sbjct: 89 VADLEGGIAGFAFASGMAAEATVLELLDHGSHIVASDDLYGGTWRLLERVRKRTAGHSVT 148 Query: 133 FVDLTDPAAFKAAI-RADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASP 191 FVD+TD A KAA+ + T+++W+E+PTNP+LK+ D+AAIA I + G LTV D+TFASP Sbjct: 149 FVDVTDLDAVKAAVQKGKTRVIWVESPTNPLLKVPDLAAIAAIGKSAGALTVADSTFASP 208 Query: 192 MLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDS 251 ++Q+PL LG D+V+HSATKYL+GHSD++ G+ V + A LA+ + FLQN+ G V PF + Sbjct: 209 VIQKPLDLGFDIVLHSATKYLSGHSDIIAGVVAVKEPA-LADALRFLQNATGAVLDPFPA 267 Query: 252 FLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGG 311 FLALRGLKTL LR+ H NALA+AQ LE HP +++VIYPGL SHPQH +A RQM+GFGG Sbjct: 268 FLALRGLKTLALRIERHSANALAIAQSLEGHPKLKRVIYPGLKSHPQHQVAARQMNGFGG 327 Query: 312 IVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDA 371 +++I + +R E LFTLAESLGGVESL HP M+H S+P RR+ LGI Sbjct: 328 MLTIDIDTDEGGVRRVLENLNLFTLAESLGGVESLAGHPYTMSHGSLPPERRDALGIGWG 387 Query: 372 LVRLSVGIEDLGDLRGDLERAL 393 LVRLS GIED GDL DL +AL Sbjct: 388 LVRLSAGIEDAGDLIADLRQAL 409 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: 543 Number of extensions: 29 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: 397 Length of database: 412 Length adjustment: 31 Effective length of query: 366 Effective length of database: 381 Effective search space: 139446 Effective search space used: 139446 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 10 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