Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate GFF2323 PGA1_c23540 O-succinylhomoserine sulfhydrylase MetZ
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Phaeo:GFF2323 Length = 396 Score = 265 bits (677), Expect = 2e-75 Identities = 147/355 (41%), Positives = 220/355 (61%), Gaps = 7/355 (1%) Query: 41 ATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVM-ELL 99 A + + ++ P E F Y+R NPT +E +AALEG AFA ASGMAA + + +L Sbjct: 42 AEARFIETGPDE---FIYARYGNPTVAMFEERIAALEGAEDAFATASGMAAVNGALTSIL 98 Query: 100 DAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPT 159 AG HVV+ L+G + E + R G++ +FVD TD A++AA+R DTK V+ E+ + Sbjct: 99 KAGDHVVSAKALFGSCLYILENILTRY-GVEVTFVDGTDLDAWRAALRPDTKAVFFESMS 157 Query: 160 NPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMV 219 NP L+++DIAA+A +A G VVDN F++P+ + GAD+V++SATK+++G ++ Sbjct: 158 NPTLEVIDIAAVAELAHAVGATVVVDNVFSTPVFSNAIEQGADVVIYSATKHIDGQGRVL 217 Query: 220 GGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWL 279 GG+ ++G + + GG PF+++ L+GL+T+ LR+ A E AL LAQ L Sbjct: 218 GGV-ILGTRDFIRGTVEPYMKHTGGSLSPFNAWTLLKGLETISLRVNAQAETALELAQAL 276 Query: 280 ETHPAIEKVIYPGLASHPQHVLAKRQMSGFGG-IVSIVLKGGFDAAKRFCEKTELFTLAE 338 HPA+ +++YPGL H QH L +RQ+ G GG ++S+ LKGG DAA RF + ++ Sbjct: 277 SGHPALSRLMYPGLEDHAQHALVQRQLGGKGGTVLSLDLKGGKDAAFRFLNALTIPVISN 336 Query: 339 SLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 +LG +S+ HPA TH + + +LGI+ LVR SVG+ED GDL DL +AL Sbjct: 337 NLGDAKSIATHPATTTHQRLSEELKSELGITPGLVRFSVGLEDAGDLIADLTQAL 391 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: 434 Number of extensions: 24 Number of successful extensions: 5 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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