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_RS33835 BPHYT_RS33835 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__BFirm:BPHYT_RS33835 Length = 396 Score = 249 bits (635), Expect = 1e-70 Identities = 151/431 (35%), Positives = 229/431 (53%), Gaps = 45/431 (10%) Query: 4 HFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPT 63 +FDT+ + +G N H I+ T+S+VFE++ ++ F Y YSRF NPT Sbjct: 6 NFDTLAVRSGTVRSDFNEHSEA---IFLTSSFVFESAADAAEKFKNSEDNYTYSRFTNPT 62 Query: 64 SNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFK 123 ++ ++R+AALEGG A +A +SG AA + GD++VS+ L+G T F F Sbjct: 63 VSMFQDRLAALEGGEACMATASGMAAIMSVVMSTLQAGDHLVSSQALFGSTLGMFSQIFS 122 Query: 124 RFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVD 183 +FGI FV+ + + ++ TK +LET NP V D E I IA+ VVD Sbjct: 123 KFGITTTFVDPTDLDAWKNAVRPETKMFFLETPSNPLTEVADIEAISKIANASNALFVVD 182 Query: 184 NTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQP 243 N F QP+K GAD+V HSATK++ G G +GG +V S +F + + FP Sbjct: 183 NCF-CSPALQQPLKLGADVVMHSATKFLDGQGRVLGGALVGSKQFIME---KVFP----- 233 Query: 244 AEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENA 303 +R GP ++ F +++LL+G+ETLSLR E+ NA Sbjct: 234 -------------------------FVRSAGPTLSAFNAWVLLKGMETLSLRVEKQSANA 268 Query: 304 LKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVK-DLPNADKETDPF 362 L++A+WLE P V+ V YPGL SH H A + G G +LSF +K D P + Sbjct: 269 LEIARWLEAHPAVNRVFYPGLESHPQHALAMRQQKAG-GAILSFELKGDTP------EQM 321 Query: 363 KLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIE 422 + + +V+DN K+ S N+GD +T + P TTH ++ + + A+G+++ LIR++VG+E Sbjct: 322 RANAWRVIDNTKICSITGNLGDTRTTITHPATTTHGRVTPEARAAAGISEGLIRLAVGLE 381 Query: 423 FIDDIIADFQQ 433 DI D ++ Sbjct: 382 NAGDIRGDLER 392 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: 418 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 396 Length adjustment: 32 Effective length of query: 412 Effective length of database: 364 Effective search space: 149968 Effective search space used: 149968 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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