Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_057508709.1 ABB28_RS11200 O-succinylhomoserine (thiol)-lyase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_001431535.1:WP_057508709.1 Length = 412 Score = 255 bits (651), Expect = 2e-72 Identities = 147/379 (38%), Positives = 203/379 (53%), Gaps = 23/379 (6%) Query: 7 TKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLEN 66 T + G D G V+ PI LS+ + G G +DY R+ NPTR L+ +A+A LE Sbjct: 15 TAAVRAGIDRDSAYGAVTPPIVLSSNFSFDGFGNKRQYDYTRSGNPTRDLLGEALAELEG 74 Query: 67 GARGLAFSSGMAAIQTIM-ALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSD 125 GA G+ ++GM AI ++ AL D L+V D YGG++RLF K D +D Sbjct: 75 GAGGVVTATGMGAISLVLQALLGPEDTLVVPHDAYGGSWRLFNALAGKGQFKLVTADLTD 134 Query: 126 EDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLE 185 L + + K V VETP+NPL++ D+ + + G L++VDNTF +P LQ+PL Sbjct: 135 PRSLAQALAGSPKLVLVETPSNPLLRITDLRFVIDAAHKAGALVVVDNTFLSPALQQPLA 194 Query: 186 LGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMK 245 GAD+V+HS TKY+ GH+D++ G VV +D L +++ NA+G PFD++L +RG++ Sbjct: 195 FGADLVLHSTTKYINGHSDVVGGAVVARDPELAQQLTWWANALGLTGSPFDAFLTLRGLR 254 Query: 246 TLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRL-- 287 TL R+R HQ N + L +S V YPG G MLSF L Sbjct: 255 TLDARLRVHQENTAAIVPLLAAHRAVSAVYYPGLADHPGHAIAARQQSGFGAMLSFELVT 314 Query: 288 ----QKEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLR 343 V F+ L+ AESLGGVES + +PAT TH + + R A G+ LLR Sbjct: 315 CDGDDPHAAVRAFVDGLQYFTLAESLGGVESLVAHPATMTHAAMTVQARQAAGISEGLLR 374 Query: 344 FSVGIEHAEDLKEDLKQAL 362 SVGIE DL DL AL Sbjct: 375 LSVGIESERDLLADLAAAL 393 Lambda K H 0.319 0.135 0.392 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: 341 Number of extensions: 14 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: 373 Length of database: 412 Length adjustment: 31 Effective length of query: 342 Effective length of database: 381 Effective search space: 130302 Effective search space used: 130302 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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