Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate CA265_RS06375 CA265_RS06375 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__Pedo557:CA265_RS06375 Length = 379 Score = 318 bits (815), Expect = 2e-91 Identities = 168/374 (44%), Positives = 231/374 (61%), Gaps = 18/374 (4%) Query: 7 TKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLEN 66 TK G D TG V PIY ++ Y + G++ G++Y R NPTR+ +ED +A LEN Sbjct: 5 TKAIHAGQEPDPTTGAVMTPIYQTSTYWQKSPGDNKGYEYSRGTNPTRKALEDCLAALEN 64 Query: 67 GARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSDE 126 GLAFSSGM A ++ L + GDE+I +DLYGG+YR+F + KYG+ FH+ D S Sbjct: 65 AKYGLAFSSGMGATDAVLKLLQPGDEVITGNDLYGGSYRIFTKIFTKYGIKFHFLDLSKP 124 Query: 127 DCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLEL 186 + + I TK V++ETPTNP MQ DIE +A+ITKE L+L VDNTF +P LQ P++L Sbjct: 125 ENILPYINDKTKLVWIETPTNPTMQIIDIEGVAKITKEKNLILTVDNTFASPYLQNPIDL 184 Query: 187 GADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKT 246 GADIV+HS TKY+GGH+D++ G +V DE+L ++++ NA GA P D++L++RG+KT Sbjct: 185 GADIVMHSVTKYIGGHSDVVMGALVTNDEQLYKDLWFIYNACGATPGPQDAFLVLRGIKT 244 Query: 247 LSLRMRQHQANAQELAAFLEEQEEISDVLYP----------------GKGGMLSFRLQKE 290 L LRM+ H N + +A +L+ ++ + +P G GGM+S L+ Sbjct: 245 LHLRMKAHCENGERIAHYLKTHPKVDKIYWPGFEDHPNHDIAKKQMRGFGGMISITLKGA 304 Query: 291 EWVNPF--LKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGI 348 + F K AESLGGVES I +PAT TH IP+E R GV + LLR SVG+ Sbjct: 305 DLEETFRISSNFKVFTLAESLGGVESLINHPATMTHGSIPKEEREKVGVTDNLLRLSVGV 364 Query: 349 EHAEDLKEDLKQAL 362 E +DL EDL AL Sbjct: 365 EDIDDLLEDLANAL 378 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: 394 Number of extensions: 13 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: 379 Length adjustment: 30 Effective length of query: 343 Effective length of database: 349 Effective search space: 119707 Effective search space used: 119707 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