Align Succinate-acetate/proton symporter SatP; Succinate-acetate transporter protein (characterized)
to candidate BPHYT_RS27785 BPHYT_RS27785 hypothetical protein
Query= SwissProt::P0AC98 (188 letters) >FitnessBrowser__BFirm:BPHYT_RS27785 Length = 201 Score = 160 bits (406), Expect = 1e-44 Identities = 86/185 (46%), Positives = 115/185 (62%), Gaps = 6/185 (3%) Query: 3 NTKLANPAPLGLMGFGMTTILLNLHNVGYFALD--GIILAMGIFYGGIAQIFAGLLEYKK 60 N K NPA LGL GF +TT LL++ N G+F + G++LA+ YGG AQ+ AGL+E + Sbjct: 2 NIKAPNPASLGLAGFALTTWLLSMINAGWFNGESMGMVLAVAFAYGGTAQMIAGLMEIPR 61 Query: 61 GNTFGLTAFTSYGSFWLTLVAILLMPKLGLTDAPNAQFLGVYLGLWGVFTLFMFFGTLKG 120 GN FG TAF SYG+FW +L +L L A F+G YL LWG+FTL+M+ T + Sbjct: 62 GNAFGATAFLSYGAFWWSLALFVLF----LHGNVPAAFIGWYLFLWGMFTLYMWVATWRA 117 Query: 121 ARVLQFVFFSLTVLFALLAIGNIAGNAAIIHFAGWIGLICGASAIYLAMGEVLNEQFGRT 180 AR LQ VF SL + F +LA G A + H G++GL+ A YL+ E++NE GR Sbjct: 118 ARALQLVFLSLWLTFFVLAASEWTGLAWLHHAGGYLGLVTALLAFYLSAAEIINETHGRV 177 Query: 181 VLPIG 185 VLP+G Sbjct: 178 VLPVG 182 Lambda K H 0.330 0.147 0.457 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: 166 Number of extensions: 12 Number of successful extensions: 3 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: 188 Length of database: 201 Length adjustment: 20 Effective length of query: 168 Effective length of database: 181 Effective search space: 30408 Effective search space used: 30408 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 44 (21.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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