Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate BWI76_RS00785 BWI76_RS00785 cystathionine gamma-synthase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Koxy:BWI76_RS00785 Length = 386 Score = 317 bits (811), Expect = 5e-91 Identities = 175/374 (46%), Positives = 236/374 (63%), Gaps = 3/374 (0%) Query: 18 ATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALE 77 AT+A+ G + D G V+PPI+ +STY + E + +YSR NPTR +R +A LE Sbjct: 6 ATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELE 65 Query: 78 GGTRAFAFASGMAATSTVMEL-LDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDL 136 GG A +GM+A V + L G +VA D YGG++RLF+ + +R FVD Sbjct: 66 GGAGAVLTNTGMSAILLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGC-YRVLFVDQ 124 Query: 137 TDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRP 196 D A AA+ K+V +E+P+NP+L++VDIA I +AR+ G ++VVDNTF SP LQ P Sbjct: 125 NDEQALSAALAEKPKLVLVESPSNPLLRVVDIAKICGLAREAGAVSVVDNTFLSPALQNP 184 Query: 197 LSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALR 256 L+LGADLV+HS TKYLNGHSD+V G+ + D A + E +A+ N+IG G FDS+L LR Sbjct: 185 LALGADLVLHSCTKYLNGHSDVVAGVVIAKDPATVTE-LAWWANNIGVTGGAFDSYLLLR 243 Query: 257 GLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIV 316 GL+TL RM NALA+ +L+T P ++K+ +P L + H +A RQ GFG ++S Sbjct: 244 GLRTLSPRMEVAQRNALAIVDYLKTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFE 303 Query: 317 LKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLS 376 L G +RF LFTLAESLGGVESL++H A MTHA + R GIS+ L+R+S Sbjct: 304 LDGDEQTLRRFLSGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRIS 363 Query: 377 VGIEDLGDLRGDLE 390 GIED DL DLE Sbjct: 364 TGIEDGEDLIADLE 377 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: 422 Number of extensions: 20 Number of successful extensions: 4 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: 386 Length adjustment: 31 Effective length of query: 366 Effective length of database: 355 Effective search space: 129930 Effective search space used: 129930 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