Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate BWI76_RS16730 BWI76_RS16730 cystathionine gamma-lyase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Koxy:BWI76_RS16730 Length = 395 Score = 378 bits (970), Expect = e-109 Identities = 190/380 (50%), Positives = 256/380 (67%), Gaps = 1/380 (0%) Query: 13 RALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERC 72 R +ATLA+H G DP T A+ PI S++ Q + E F YSR NPTR AYE Sbjct: 4 RTKDIATLAVHAGNQSDPVTHAIFTPIVTASSFIQPNLYEGGDFCYSRVSNPTRKAYESA 63 Query: 73 VAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFS 132 +A LEGG A A ASGMAAT+ VMELL +H++AM +YGGT+RLFE+++ T G+ S Sbjct: 64 LAELEGGIYATATASGMAATNIVMELLPKDAHIIAMKGVYGGTWRLFEKLKTHTTGVTIS 123 Query: 133 FVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPM 192 ++DL D + I+ +T ++WIETPTNP+L+LVDIA + IA++ + T VDNTFAS Sbjct: 124 YIDLNDEQSLINTIQENTALIWIETPTNPLLELVDIAKVCRIAKERAITTCVDNTFASAW 183 Query: 193 LQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSF 252 +PL +GAD+V+ S +KY+ GHSD++GG AV+ +N LA ++ F++ ++G + PFD++ Sbjct: 184 NHKPLEMGADMVMLSTSKYVGGHSDLIGG-AVITNNEALASRLDFIKTTLGSIASPFDAY 242 Query: 253 LALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGI 312 LALRG+KTL LRM C NAL +AQ+LE HPAI V YPGL SHPQH L ++QM G + Sbjct: 243 LALRGMKTLDLRMARQCGNALRVAQYLENHPAIASVYYPGLPSHPQHQLCRQQMRSGGAV 302 Query: 313 VSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDAL 372 V+ LKG + KRF F LAESLGGVES++NH A M+H ++ RE +G+ D Sbjct: 303 VTATLKGDIQSLKRFIGGLHYFVLAESLGGVESMINHSASMSHGAMSKEEREAIGVYDTT 362 Query: 373 VRLSVGIEDLGDLRGDLERA 392 +R SVGIE + DL DLE A Sbjct: 363 LRFSVGIEHIDDLLQDLESA 382 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: 465 Number of extensions: 21 Number of successful extensions: 2 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: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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