Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Ga0059261_1458 Ga0059261_1458 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Korea:Ga0059261_1458 Length = 440 Score = 231 bits (589), Expect = 3e-65 Identities = 153/412 (37%), Positives = 219/412 (53%), Gaps = 33/412 (8%) Query: 11 GDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSS---------------PGEHQG 55 G R LS ATL + G P S G++ PPI+ATST+ + PG +G Sbjct: 30 GGRQLSPATLMMGHGYDPMLSEGSLKPPIFATSTFVFPNAAAGKRHFEGVTGKRPGGAEG 89 Query: 56 FEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTV-MELLDAGSHVVAMDDLYGG 114 YSR + P + E + E A AF+SGM+A +T+ + ++ G +V LY Sbjct: 90 LVYSRFNGPNQEILEDRLGIWEEAEDALAFSSGMSAIATLFLAMVKPGDTIVHSGPLYAA 149 Query: 115 TFRLFERVRRRTA--GLDFSFVDLTDP--AAFKAAIRADTKMVWIETPTNPMLKLVDIAA 170 T L R+ + LDF + A A + ++++E+P NP LVD+ A Sbjct: 150 TETLIARILGKFGVHWLDFPAGATREEIDAVLSKAASGNVALIYLESPANPTNALVDVEA 209 Query: 171 IAVIARKHGLLT-------VVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIA 223 +A A + + T +DNTF P+ +PL GADLVV+S TKY GHSD+V G Sbjct: 210 VA--ASRDAIFTGASKPPIAIDNTFLGPLWAKPLQQGADLVVYSLTKYAGGHSDLVAG-G 266 Query: 224 VVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHP 283 V+G EL + ++N+IG + P +++ LR L+TL LRM ENA+ + ++L THP Sbjct: 267 VLGSK-ELINTIRLMRNTIGTICDPNTAWMLLRSLETLELRMSRAGENAIKVCEYLRTHP 325 Query: 284 AIEKVIYPGLASHP--QHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLG 341 +E V Y G Q + R +G G S+ LKGG A F + ++ LA SLG Sbjct: 326 KVESVGYLGFLPEGSRQRDIYDRHCTGAGSTFSLYLKGGEKEAFAFLDSLKIAKLAVSLG 385 Query: 342 GVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 G E+L + PA MTH S+P AR++ LGI+D LVR+S+G+ED DL D E AL Sbjct: 386 GTETLASAPAAMTHLSVPDARKKALGITDNLVRISIGVEDADDLIADFEEAL 437 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: 467 Number of extensions: 22 Number of successful extensions: 6 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: 440 Length adjustment: 32 Effective length of query: 365 Effective length of database: 408 Effective search space: 148920 Effective search space used: 148920 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