Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Dsui_2042 Dsui_2042 cystathionine beta-lyase/cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__PS:Dsui_2042 Length = 392 Score = 291 bits (745), Expect = 2e-83 Identities = 167/387 (43%), Positives = 221/387 (57%), Gaps = 27/387 (6%) Query: 3 QHVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGE-----STGFDYVRTKNPTRQLV 57 Q T+ G D TG VS PIY ++ Y + E FDY R+ NPTR + Sbjct: 5 QGFATRAIHAGQEPDPTTGAVSIPIYATSTYVQPALNEPKQYAGATFDYARSANPTRLAL 64 Query: 58 EDAIANLENGA----RGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFEN-EWK 112 E IA+LE GA G AF+SG+AA T++ L +G ++ S DLYGG+ RLF Sbjct: 65 ERCIADLEGGAFATATGFAFASGLAASATVLELLPAGSHVVASDDLYGGSVRLFNRVRSN 124 Query: 113 KYGLTFHYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVD 172 L Y DFS + + + ITP TK ++VETP+NPL++ D++ +A I K+ GLL + D Sbjct: 125 SADLKVTYADFSSRESIEAAITPETKLLWVETPSNPLLKLVDLDLVAAIGKDRGLLTVAD 184 Query: 173 NTFYTPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVL 232 NTF +P +QRPLE G DIV+HSATKYL GH+D++AG+ V L E + QNA GAVL Sbjct: 185 NTFASPWIQRPLEHGFDIVVHSATKYLNGHSDVIAGVAVTARADLAERLAFLQNAAGAVL 244 Query: 233 PPFDSWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGKGGMLSFRLQKEEW 292 PFD++L +RG+KTL+LRM +H ANA+ +A +LE+ I V YPG L K + Sbjct: 245 GPFDAFLALRGLKTLALRMERHCANAEAIARWLEQHPAIEKVHYPGLASHPQHELAKRQM 304 Query: 293 -----------------VNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIAN 335 L+ K AESLGGVES I PA TH +P E R Sbjct: 305 RGFGGMVSAVVKGGLPAAKKLLENTKIFVLAESLGGVESLIELPALMTHASVPPEQRRRI 364 Query: 336 GVCNRLLRFSVGIEHAEDLKEDLKQAL 362 G+ + L+R SVG+E EDL DL+QAL Sbjct: 365 GIDDGLVRLSVGVEDVEDLLADLEQAL 391 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: 383 Number of extensions: 19 Number of successful extensions: 5 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 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