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 BPHYT_RS13720 BPHYT_RS13720 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__BFirm:BPHYT_RS13720 Length = 450 Score = 338 bits (866), Expect = 3e-97 Identities = 181/434 (41%), Positives = 270/434 (62%), Gaps = 14/434 (3%) Query: 3 SHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNP 62 + FDT+ LHAG D +RA PIY TTS+ F +S H + LF +E G+VYSR NP Sbjct: 4 NRFDTLALHAGAAP--DPTTGARATPIYQTTSFSFRDSDHAAALFNMERAGHVYSRISNP 61 Query: 63 TSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISF 122 T V EER+AALE GA A+ +SGQAA LAI L G +IV++S LYGG++N + Sbjct: 62 TVAVFEERVAALENGAGAIGTASGQAALHLAIATLMGAGSHIVASSALYGGSHNLLHYTL 121 Query: 123 KRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVV 182 +RFGIE FV+ + + + T+ ++ ET+GNP +V D + IAH+H +P++V Sbjct: 122 RRFGIETTFVKPGDLDAWRAALRPNTRLLFGETLGNPGLDVLDIAAVAQIAHEHRVPLLV 181 Query: 183 DNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQ 242 D+TF Y +P ++GAD V HSATK++GGHGTTIGG++VD G F + + +FP+F++ Sbjct: 182 DSTF-TTPYLLKPFEHGADFVYHSATKFLGGHGTTIGGVLVDGGTFDF-EASGRFPEFTE 239 Query: 243 PAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGEN 302 P +G+HG +++E +++ R E LRD G ++P A++ LLQG+ETL LR ERH N Sbjct: 240 PYDGFHGMVFSEESTVAPFLLRARREGLRDFGACLHPQAAWQLLQGIETLPLRMERHVAN 299 Query: 303 ALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPF 362 ++ ++L V V+YP L +H H AK+ L G G V SF ++ Sbjct: 300 TRRVVEFLAAHAAVESVAYPELPTHPDHALAKRLLPRGAGAVFSFNLRG----------D 349 Query: 363 KLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIE 422 + +G ++ L L S+LANVGDA++LVI P TTH +++ A+G+ + IR+S+G+E Sbjct: 350 RAAGRSFIEALSLFSHLANVGDARSLVIHPASTTHFRMDAAALAAAGIAEGTIRLSIGLE 409 Query: 423 FIDDIIADFQQSFE 436 DD+I D +++ + Sbjct: 410 DPDDLIDDLKRALK 423 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: 505 Number of extensions: 17 Number of successful extensions: 4 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: 450 Length adjustment: 33 Effective length of query: 411 Effective length of database: 417 Effective search space: 171387 Effective search space used: 171387 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