Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_043745532.1 AMB_RS21365 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000009985.1:WP_043745532.1 Length = 403 Score = 263 bits (672), Expect = 7e-75 Identities = 154/362 (42%), Positives = 224/362 (61%), Gaps = 9/362 (2%) Query: 39 IYATSTYAQSS-PGEHQGFEYSRTHNPTRFAYERCVAALEGG-----TRAFAFASGMAAT 92 +Y ++ A++S G YSR NPT +E+ +A +EG A A ASGMAA Sbjct: 42 VYDSAEEAEASFDGTLDRMVYSRFKNPTVAVFEQRLAEMEGAPPGMAVAARATASGMAAV 101 Query: 93 -STVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTK 151 + ++ L AG VVA L+G + + R G++ FVD TD +++AA+ T Sbjct: 102 HAALLCQLRAGDRVVASTALFGSCHWIINELLPRY-GVERVFVDGTDLKSWEAALSRPTA 160 Query: 152 MVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKY 211 V++ETP+NP L+++D+AA+ +A K G VVDN FA+P+LQ PL LGAD+VV+SATK+ Sbjct: 161 CVFLETPSNPTLEIIDLAAVCELAHKAGAKVVVDNVFATPILQSPLELGADIVVYSATKH 220 Query: 212 LNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCEN 271 ++G +GG AV+G A+ + + G PF++++ L+GL+TL LRM HC N Sbjct: 221 MDGQGRCLGG-AVLGSPEFCADILGPFLRNTGPALSPFNAWVLLKGLETLDLRMERHCAN 279 Query: 272 ALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKT 331 AL +A++LE P + +V+YPGL SHPQH LAKRQM G+G IV++ LKGG AA + Sbjct: 280 ALKVARFLEARPEVARVLYPGLESHPQHDLAKRQMRGWGSIVALELKGGKPAAYKLLNGV 339 Query: 332 ELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLER 391 EL ++ +LG +SL+ HP TH + + +GI++ L+RLSVG+ED DL DL R Sbjct: 340 ELIDISNNLGDAKSLITHPWTTTHQRLSPEDKLSMGITEGLLRLSVGLEDGDDLVEDLGR 399 Query: 392 AL 393 AL Sbjct: 400 AL 401 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: 457 Number of extensions: 18 Number of successful extensions: 3 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: 403 Length adjustment: 31 Effective length of query: 366 Effective length of database: 372 Effective search space: 136152 Effective search space used: 136152 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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