Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate SMc02595 SMc02595 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__Smeli:SMc02595 Length = 408 Score = 256 bits (653), Expect = 1e-72 Identities = 142/378 (37%), Positives = 205/378 (54%), Gaps = 17/378 (4%) Query: 2 SQHVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAI 61 S ET A G +D G+V P+YLS+ Y G +DY R+ NPTR L+ A+ Sbjct: 28 SDRAETTAAAHGVATDPAFGSVVPPLYLSSTYEFAGFDTPRAYDYGRSGNPTRDLLAQAL 87 Query: 62 ANLENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYD 121 A LE GA + SGMAA+ ++ + ++ D YGGT RL + LTF Sbjct: 88 AKLEGGADAVVTPSGMAALDLLLGRLRRNHLVLAPHDCYGGTLRLLKARADLGHLTFRLT 147 Query: 122 DFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQ 181 D D + ++ V +E+P+NPLM+ DI ++ + K G + VDNTF +P LQ Sbjct: 148 DQRDFGGFEAALSDAPALVLIESPSNPLMRVTDIARLSTLAKAAGSAVAVDNTFLSPALQ 207 Query: 182 RPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLM 241 +PL LGAD IHSATK+L GH+D++AG V+ + + ++ + N GAV PFD+WL + Sbjct: 208 QPLSLGADYAIHSATKFLNGHSDVIAGAVIAAEPQEAHDLKRWANVTGAVAAPFDAWLTL 267 Query: 242 RGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSF 285 RG++TL RM + +A +A +L+ + V Y G G M+SF Sbjct: 268 RGLRTLFARMSSQERSAMTIAEYLDAHPAVRHVHYAGLPDHADHEVARRQQRGFGAMMSF 327 Query: 286 RLQ-KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRF 344 L+ V FL ++ AESLGGVES + +PAT TH+D+ E R G+ + LLR Sbjct: 328 ELEGGVPAVRRFLAHIRCFTLAESLGGVESLVAHPATMTHLDMGPEARERAGIRDELLRL 387 Query: 345 SVGIEHAEDLKEDLKQAL 362 S+G+EH +DL E L+ L Sbjct: 388 SIGLEHIDDLMEGLELGL 405 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: 356 Number of extensions: 15 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: 373 Length of database: 408 Length adjustment: 31 Effective length of query: 342 Effective length of database: 377 Effective search space: 128934 Effective search space used: 128934 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 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