Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate BWI76_RS24210 BWI76_RS24210 cystathionine gamma-lyase
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__Koxy:BWI76_RS24210 Length = 381 Score = 299 bits (765), Expect = 1e-85 Identities = 163/378 (43%), Positives = 236/378 (62%), Gaps = 20/378 (5%) Query: 4 HVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIAN 63 ++ T G +DE G V PIY ++ + G+ TG++Y R+ NPTR +E AIA+ Sbjct: 3 NLHTLSVHSGTFTDE-HGAVMPPIYATSTFAQPAPGQHTGYEYSRSGNPTRHALETAIAD 61 Query: 64 LENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKY-GLTFHYDD 122 LE+G RG AF+SG+AAI T++ L L+ D+YGGTYRL EN ++ GL + Sbjct: 62 LESGTRGYAFASGLAAISTVLELLDKDSHLVAVDDVYGGTYRLIENVRRRSAGLRVSWVK 121 Query: 123 FSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQR 182 D + + I P+T+ ++VETPTNPL++ AD+ IA I + H ++ + DNTF +P + R Sbjct: 122 PDDLAAIEAAIRPDTRMIWVETPTNPLLKLADLSAIAAIARRHNIISVTDNTFASPAIHR 181 Query: 183 PLELGADIVIHSATKYLGGHNDLLAGLVVVKDE-RLGEEMFQHQNAIGAVLPPFDSWLLM 241 PLELG DIV+HSATKYL GH+D++AGL VV D L E++ QNA+G VL PF S+L + Sbjct: 182 PLELGFDIVVHSATKYLNGHSDVVAGLAVVGDNAALAEKLGYLQNAVGGVLDPFSSFLTL 241 Query: 242 RGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPG----------------KGGMLSF 285 RG++TL+LRM +H +NA LA +LE+Q ++ V +P GGM+S Sbjct: 242 RGIRTLALRMERHSSNALLLAEWLEQQPQVEKVWFPWLASHPHHQLARRQMALPGGMISV 301 Query: 286 RLQKEE-WVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRF 344 ++ ++ + ++ LK AESLGGVES ++ P + TH IP E R+ANG+ +L+R Sbjct: 302 VVKGDDSYAERIIRKLKLFTLAESLGGVESLVSQPFSMTHASIPLEQRLANGITPQLIRL 361 Query: 345 SVGIEHAEDLKEDLKQAL 362 SVGIE +DL D + AL Sbjct: 362 SVGIEDPQDLIADWRHAL 379 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: 351 Number of extensions: 15 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: 381 Length adjustment: 30 Effective length of query: 343 Effective length of database: 351 Effective search space: 120393 Effective search space used: 120393 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