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 WP_012406802.1 BPHY_RS38375 PLP-dependent transferase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000020045.1:WP_012406802.1 Length = 440 Score = 300 bits (767), Expect = 8e-86 Identities = 176/449 (39%), Positives = 264/449 (58%), Gaps = 27/449 (6%) Query: 1 MPSHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHG-SQLFGLEVPGYVYSRF 59 +P +T L+AG + D ++ +VPIY +T+Y E + ++ + G+ YSR Sbjct: 8 VPMSRETALLYAGYRH--DPVTKAVSVPIYQSTAYELEGDLEKIAGIYNAKEDGFTYSRI 65 Query: 60 QNPTSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAH--TGDNIVSTSYLYGGTYNQ 117 NPT+ +LE+R AA+E + +LAV+SGQAA LAI L GDN+V++ YLYG ++N Sbjct: 66 INPTTRILEKRFAAVESASDSLAVASGQAATFLAIANLCSGTPGDNVVASKYLYGNSWNL 125 Query: 118 FKISFKRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHG 177 +FKR GIEAR + N FE + D+RT A++ E NP + I +HG Sbjct: 126 LFNTFKRLGIEARCADPKNISSFELLTDDRTIAIFGEAFSNPCLVPLPIAALAEIGKRHG 185 Query: 178 IPVVVDNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKF 237 +PV+VDNT C+P GA I T+SATK++ GHGTT+GG+IVD+G+F + D +F Sbjct: 186 VPVIVDNT--TTPLVCRPASLGASISTYSATKYLCGHGTTLGGLIVDNGRFAFDD-TVRF 242 Query: 238 PQFSQPAEGYHGTIYNEA------YGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVET 291 P F +P E + G ++ EA G Y++ R LRD G ++PF+SF L+QG+ET Sbjct: 243 PLFHEPDEAHGGILWKEAVLKLDDLGASPYLLKARMTWLRDTGAAISPFSSFQLIQGLET 302 Query: 292 LSLRAERHGENALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYL--SNGFGGVLSFGV 349 L LR +RH ENAL +A++L + P V VSYP L+ E + + S G+G ++ F + Sbjct: 303 LHLRMQRHCENALAVAEFLIKHPKVKRVSYPSLSYGYERELVDELVDTSVGYGAIIMFEL 362 Query: 350 KDLPNADKETDPFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASG 409 D + +G + + N+ L +++NVGDA+TLV P TTH + +++ A+G Sbjct: 363 AD-----------EAAGRRFITNIDLMYHVSNVGDARTLVTHPVSTTHTTVPKEQREAAG 411 Query: 410 VTKDLIRVSVGIEFIDDIIADFQQSFETV 438 + IR+ VGIE +DDI+AD QQ + V Sbjct: 412 IFDGSIRLCVGIENVDDIVADIQQGLDAV 440 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: 534 Number of extensions: 20 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: 440 Length adjustment: 32 Effective length of query: 412 Effective length of database: 408 Effective search space: 168096 Effective search space used: 168096 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