Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_011602019.1 FRAAL_RS03375 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000058485.1:WP_011602019.1 Length = 392 Score = 276 bits (706), Expect = 7e-79 Identities = 162/377 (42%), Positives = 222/377 (58%), Gaps = 23/377 (6%) Query: 6 ETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTG-FDYVRTKNPTRQLVEDAIANL 64 ET G D TG V+ P++LS+ + G+G G F+Y R+ NPTR +E +A L Sbjct: 11 ETIAIHAGQDPDPGTGAVAPPLHLSSTFAQDGVGGLRGGFEYSRSGNPTRAALETCLAAL 70 Query: 65 ENGARGLAFSSGMAAIQTIM-ALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDF 123 E G GLAFS+GMAA T++ A+ + GD +I+ +D YGGTYRL ++G+ D Sbjct: 71 EGGRVGLAFSAGMAATDTLLRAVCRPGDHVIIPADAYGGTYRLIARVLGEWGVEHSSVDL 130 Query: 124 SDEDCLRSKITPN-TKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQR 182 +D + R+ + P T+ V+ ETPTNPL+ ADI +A + + G LL VDNTF +P LQ+ Sbjct: 131 TDLEATRAAVRPGVTRLVWCETPTNPLLTIADIAALASLAHDAGALLAVDNTFASPYLQQ 190 Query: 183 PLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMR 242 PL LGAD V+HS TKYLGGH+D++ G +VV D LG ++ QNA GAV PFD WL++R Sbjct: 191 PLALGADAVVHSTTKYLGGHSDVVGGAIVVSDPELGTQLRFLQNAAGAVPGPFDCWLVLR 250 Query: 243 GMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFR 286 G+KTL++RM +H ANA+ +A L +S V YPG GGM+S Sbjct: 251 GIKTLAVRMDRHCANARGVATLLAAHPAVSTVYYPGLPGHAGHGIAAKQMRDFGGMVSLT 310 Query: 287 LQK-EEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFS 345 L+ + AESLGGVES I +PA+ TH + + V L+R S Sbjct: 311 LRDGPRAAVELCGRTRLFTLAESLGGVESLIEHPASMTHASV---VNSPLAVPAELVRLS 367 Query: 346 VGIEHAEDLKEDLKQAL 362 VGIE A+DL DL++AL Sbjct: 368 VGIESADDLAADLRRAL 384 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: 370 Number of extensions: 15 Number of successful extensions: 6 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: 392 Length adjustment: 30 Effective length of query: 343 Effective length of database: 362 Effective search space: 124166 Effective search space used: 124166 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