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 AZOBR_RS11340 AZOBR_RS11340 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__azobra:AZOBR_RS11340 Length = 436 Score = 365 bits (937), Expect = e-105 Identities = 195/435 (44%), Positives = 269/435 (61%), Gaps = 19/435 (4%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 FDT+ LHAGQ D A +RAVPIY +TSYVF+++ H + LF LE PG++YSR NPT Sbjct: 9 FDTLSLHAGQRP--DPATGARAVPIYQSTSYVFDDTDHAASLFNLERPGHIYSRISNPTV 66 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 VLEER+AAL+GG A+ +SGQAA TLAI L G +IV++S +YGG+ N + R Sbjct: 67 AVLEERLAALDGGVGAVCTASGQAALTLAIMTLMDAGGHIVASSSIYGGSRNLLAYTLPR 126 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 FGI FV + + F T+ ++ E +GNP V D + AIAH+ G+P++VD Sbjct: 127 FGITTTFVNPRDLDGFRAAIRPETRLLFGEVLGNPGLEVLDIPSLSAIAHEAGLPLMVDA 186 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 TF Y C+P+ GAD+V HS TKW+ GHG IGG+++D G F W + KFP ++P Sbjct: 187 TF-VTPYLCKPLSVGADLVMHSCTKWLAGHGVAIGGVVIDGGTFDW-EASGKFPTLTEPY 244 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 GYHG + E YG A+++ R E LRD G M+P +F +LQGVETL LR + H N Sbjct: 245 AGYHGIDFAEEYGPAAFVMRARAEGLRDFGACMSPMNAFQILQGVETLPLRMKGHIHNTR 304 Query: 305 KLAKWLEQSPY-----VSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKET 359 K+ +LE Y V+WV++P L H H + L +G G ++SFG+K A Sbjct: 305 KVLGFLESEAYAENGSVAWVTHPELPDHPDHRLRAQLLPHGAGSIISFGIKGGREA---- 360 Query: 360 DPFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSV 419 G + ++ L L S+LANVGDAK+LVI P TTH QL+ + A+GV +D+IR+S+ Sbjct: 361 ------GRRFIEKLALFSHLANVGDAKSLVIHPASTTHAQLDAEALAAAGVGEDMIRLSI 414 Query: 420 GIEFIDDIIADFQQS 434 G+E DD+I D +Q+ Sbjct: 415 GLEDCDDLIDDLRQA 429 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: 531 Number of extensions: 19 Number of successful extensions: 6 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: 444 Length of database: 436 Length adjustment: 32 Effective length of query: 412 Effective length of database: 404 Effective search space: 166448 Effective search space used: 166448 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: 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