Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate BWI76_RS24210 BWI76_RS24210 cystathionine gamma-lyase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Koxy:BWI76_RS24210 Length = 381 Score = 470 bits (1209), Expect = e-137 Identities = 237/378 (62%), Positives = 293/378 (77%), Gaps = 1/378 (0%) Query: 16 SLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAA 75 +L TL++H G D GAVMPPIYATST+AQ +PG+H G+EYSR+ NPTR A E +A Sbjct: 3 NLHTLSVHSGTFTDEH-GAVMPPIYATSTFAQPAPGQHTGYEYSRSGNPTRHALETAIAD 61 Query: 76 LEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVD 135 LE GTR +AFASG+AA STV+ELLD SH+VA+DD+YGGT+RL E VRRR+AGL S+V Sbjct: 62 LESGTRGYAFASGLAAISTVLELLDKDSHLVAVDDVYGGTYRLIENVRRRSAGLRVSWVK 121 Query: 136 LTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQR 195 D AA +AAIR DT+M+W+ETPTNP+LKL D++AIA IAR+H +++V DNTFASP + R Sbjct: 122 PDDLAAIEAAIRPDTRMIWVETPTNPLLKLADLSAIAAIARRHNIISVTDNTFASPAIHR 181 Query: 196 PLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLAL 255 PL LG D+VVHSATKYLNGHSD+V G+AVVGDNA LAE++ +LQN++GGV PF SFL L Sbjct: 182 PLELGFDIVVHSATKYLNGHSDVVAGLAVVGDNAALAEKLGYLQNAVGGVLDPFSSFLTL 241 Query: 256 RGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSI 315 RG++TL LRM H NAL LA+WLE P +EKV +P LASHP H LA+RQM+ GG++S+ Sbjct: 242 RGIRTLALRMERHSSNALLLAEWLEQQPQVEKVWFPWLASHPHHQLARRQMALPGGMISV 301 Query: 316 VLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRL 375 V+KG A+R K +LFTLAESLGGVESLV+ P MTHASIP+ +R GI+ L+RL Sbjct: 302 VVKGDDSYAERIIRKLKLFTLAESLGGVESLVSQPFSMTHASIPLEQRLANGITPQLIRL 361 Query: 376 SVGIEDLGDLRGDLERAL 393 SVGIED DL D AL Sbjct: 362 SVGIEDPQDLIADWRHAL 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: 520 Number of extensions: 15 Number of successful extensions: 1 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: 381 Length adjustment: 30 Effective length of query: 367 Effective length of database: 351 Effective search space: 128817 Effective search space used: 128817 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