Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 17978 b3939 cystathionine gamma-synthase (NCBI)
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__Keio:17978 Length = 386 Score = 271 bits (692), Expect = 3e-77 Identities = 157/386 (40%), Positives = 215/386 (55%), Gaps = 18/386 (4%) Query: 1 MSQHVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDA 60 M++ T + G DE G V PI+LS+ Y G E DY R NPTR +V+ A Sbjct: 1 MTRKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRA 60 Query: 61 IANLENGARGLAFSSGMAAIQTIMALF-KSGDELIVSSDLYGGTYRLFENEWKKYGLTFH 119 +A LE GA + ++GM+AI + +F K GD L+ D YGG+YRLF++ K+ Sbjct: 61 LAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVL 120 Query: 120 YDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPV 179 + D DE LR+ + K V VE+P+NPL++ DI I + +E G + +VDNTF +P Sbjct: 121 FVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPA 180 Query: 180 LQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWL 239 LQ PL LGAD+V+HS TKYL GH+D++AG+V+ KD + E+ N IG FDS+L Sbjct: 181 LQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYL 240 Query: 240 LMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYP----------------GKGGML 283 L+RG++TL RM Q NAQ + +L+ Q + + +P G G ML Sbjct: 241 LLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAML 300 Query: 284 SFRLQ-KEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLL 342 SF L E+ + FL L AESLGGVES I++ AT TH + E R A G+ LL Sbjct: 301 SFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLL 360 Query: 343 RFSVGIEHAEDLKEDLKQALCQVKEG 368 R S GIE EDL DL+ +G Sbjct: 361 RISTGIEDGEDLIADLENGFRAANKG 386 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: 345 Number of extensions: 10 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: 373 Length of database: 386 Length adjustment: 30 Effective length of query: 343 Effective length of database: 356 Effective search space: 122108 Effective search space used: 122108 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