Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate CA265_RS08180 CA265_RS08180 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__Pedo557:CA265_RS08180 Length = 443 Score = 214 bits (546), Expect = 3e-60 Identities = 138/425 (32%), Positives = 219/425 (51%), Gaps = 20/425 (4%) Query: 6 TYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPT 65 +Y F T LH+ ++ GS PI+ + ++G+++A A +F K+ G Y R NPT Sbjct: 4 SYKFETLQLHAGQEIDPTTGSRAVPIYQTTSYGFKNAEHGANLFALKEFGNIYTRIMNPT 63 Query: 66 VAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMTVG 124 E +I +E G + + A+G AA + +L GD +VSS+ ++G T N + Sbjct: 64 NDVFEKRIAALEGGVAALAVASGQAAQFIALNNILEAGDSIVSSSHIYGGTYNQFKVAFK 123 Query: 125 AQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVD 184 G V + + E IT T+ +F+ETI NP V D ++I + ++ + VVD Sbjct: 124 RLGIHVDFANPDVPEEFENKITDKTKAIFLETIGNPAFSVPDFEKIAAIAKKYDLPLVVD 183 Query: 185 NTM-TSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDW--TRYPHIAENYK 241 NT YLF+P GA +VV S TK IGGHG ++GG + D G ++W ++P +E + Sbjct: 184 NTFGAGGYLFKPLEHGANIVVESATKWIGGHGTSIGGVIVDGGNYNWGNGKFPQFSEPSE 243 Query: 242 KNPAPQWG--------------MAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERE 287 + + + R + LRD G +L P + + G ET++LR +R Sbjct: 244 GYHGLVFSDVFGIGGPFGNIQFIIRARVEGLRDLGPALSPFNSFLLLQGLETLSLRVQRH 303 Query: 288 CKNALALAQMLQADERVAAVYYPGLESHPQHALSKA-LFRSFGSLMSFELKDGID-CFDY 345 NAL LA L+ V V YPGL S + L+K L FG+++SFEL + Sbjct: 304 VDNALELATWLENHPLVKEVQYPGLASSKYNNLAKKYLSNGFGAVLSFELTGSKENATQV 363 Query: 346 LNRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVA 405 ++ L+L +N+GD +TL+I + T ++ + + G+ + +RVSVG+E DD+ A Sbjct: 364 VDNLKLVSHLANVGDAKTLIIQPSATTHQQLSETEQLAAGVKPNALRVSVGIEHIDDIKA 423 Query: 406 DFRQA 410 DF QA Sbjct: 424 DFEQA 428 Lambda K H 0.319 0.134 0.391 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: 444 Number of extensions: 23 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: 413 Length of database: 443 Length adjustment: 32 Effective length of query: 381 Effective length of database: 411 Effective search space: 156591 Effective search space used: 156591 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 (21.8 bits) S2: 51 (24.3 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