Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate CA265_RS06375 CA265_RS06375 cystathionine gamma-synthase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Pedo557:CA265_RS06375 Length = 379 Score = 213 bits (541), Expect = 1e-59 Identities = 146/426 (34%), Positives = 220/426 (51%), Gaps = 55/426 (12%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F T +HAGQE D + PIY T++Y ++ S ++ GY YSR NPT Sbjct: 3 FATKAIHAGQEP--DPTTGAVMTPIYQTSTY-WQKSPGDNK-------GYEYSRGTNPTR 52 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 LE+ +AALE LA SSG A T A+ L GD +++ + LYGG+Y F F + Sbjct: 53 KALEDCLAALENAKYGLAFSSGMGA-TDAVLKLLQPGDEVITGNDLYGGSYRIFTKIFTK 111 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 +GI+ F++ PE +++TK V++ET NP + D E + I + + + VDN Sbjct: 112 YGIKFHFLDLSKPENILPYINDKTKLVWIETPTNPTMQIIDIEGVAKITKEKNLILTVDN 171 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 TF A Y PI GADIV HS TK+IGGH + G +V + + +KD Sbjct: 172 TF-ASPYLQNPIDLGADIVMHSVTKYIGGHSDVVMGALVTNDEQLYKDL----------- 219 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 IYN G P +FL+L+G++TL LR + H EN Sbjct: 220 ----WFIYNAC------------------GATPGPQDAFLVLRGIKTLHLRMKAHCENGE 257 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364 ++A +L+ P V + +PG H +H+ AKK + GFGG++S +K AD E + F++ Sbjct: 258 RIAHYLKTHPKVDKIYWPGFEDHPNHDIAKKQM-RGFGGMISITLK---GADLE-ETFRI 312 Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFI 424 S N K+ + ++G ++L+ P TH + +E+ GVT +L+R+SVG+E I Sbjct: 313 S-----SNFKVFTLAESLGGVESLINHPATMTHGSIPKEEREKVGVTDNLLRLSVGVEDI 367 Query: 425 DDIIAD 430 DD++ D Sbjct: 368 DDLLED 373 Lambda K H 0.317 0.136 0.402 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: 485 Number of extensions: 25 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 379 Length adjustment: 31 Effective length of query: 413 Effective length of database: 348 Effective search space: 143724 Effective search space used: 143724 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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