Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate HSERO_RS16440 HSERO_RS16440 hypothetical protein
Query= SwissProt::Q9WZY4 (430 letters) >FitnessBrowser__HerbieS:HSERO_RS16440 Length = 413 Score = 264 bits (675), Expect = 3e-75 Identities = 154/425 (36%), Positives = 244/425 (57%), Gaps = 18/425 (4%) Query: 2 DWKKYGYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRI 61 D K YG+ T LH+ + + GS PI+ + ++ + D+ A +F ++PG+ Y R Sbjct: 3 DKKTYGFTTTILHSDRQKGIEH-GSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQ 61 Query: 62 GNPTVSVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFR 121 GNPTV+ LE++I +E+G + A+G AAI + + GD +VS + L+G T +L+ Sbjct: 62 GNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLW- 120 Query: 122 HTLYKKSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGV 181 G V VD TD KN+E AIT T+ V++ETI NP V D + I E+ G+ Sbjct: 121 -MTVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGI 179 Query: 182 PLIVDNTV-APYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNGKFPELV 240 +VDNT+ +PY+FRP GA +VV S TK IGGHG ++GG + D+G+FDWT ++P + Sbjct: 180 LYVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT--RYPHIA 237 Query: 241 EPDPSYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCE 300 E +Y + +A+ R + LRD G + P A +G ET++LR ++ C+ Sbjct: 238 E--------NYKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECK 289 Query: 301 NALKIVEFLKSHPAVSWVNYPIAEGNKTRENAL-KYLKEGYGAIVTFGVKGGKEAGKKFI 359 NAL + + L++ V+ V YP E + ++AL K L +G++++F +K G + ++ Sbjct: 290 NALALAQMLQADERVAAVYYPGLESHP--QHALSKALFRSFGSLMSFELKDGIDC-FDYL 346 Query: 360 DSLTLISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIAD 419 + L L +N+GD RTL I A T ++ E + G+ +IR+SVG+ED +D++AD Sbjct: 347 NRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVAD 406 Query: 420 LDQAL 424 QAL Sbjct: 407 FRQAL 411 Lambda K H 0.317 0.136 0.398 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: 468 Number of extensions: 24 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: 430 Length of database: 413 Length adjustment: 32 Effective length of query: 398 Effective length of database: 381 Effective search space: 151638 Effective search space used: 151638 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