Align Succinate-acetate/proton symporter SatP; Succinate-acetate transporter protein (characterized)
to candidate 5208392 Shew_0904 GPR1/FUN34/yaaH family protein (RefSeq)
Query= SwissProt::P0AC98 (188 letters) >FitnessBrowser__PV4:5208392 Length = 188 Score = 241 bits (616), Expect = 4e-69 Identities = 113/184 (61%), Positives = 145/184 (78%) Query: 3 NTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQIFAGLLEYKKGN 62 +TKLANPAPLGLMGFGMTT+LLN+HN G+FA+D +ILAMGIFYGG+ Q+ G++ +K+G+ Sbjct: 2 STKLANPAPLGLMGFGMTTVLLNIHNAGFFAIDAMILAMGIFYGGLGQVLVGMMCFKRGD 61 Query: 63 TFGLTAFTSYGSFWLTLVAILLMPKLGLTDAPNAQFLGVYLGLWGVFTLFMFFGTLKGAR 122 TFG TAFTSYG FWLTLV ++++PKLGL A + F+G YL LWG+FT FMF G+L+ R Sbjct: 62 TFGTTAFTSYGLFWLTLVGLIMLPKLGLAAASPSHFMGWYLSLWGLFTAFMFVGSLRYPR 121 Query: 123 VLQFVFFSLTVLFALLAIGNIAGNAAIIHFAGWIGLICGASAIYLAMGEVLNEQFGRTVL 182 Q VF SLT+LF LLA + G+ I AG+ G+ CGASAIY AM +VLN+++GR +L Sbjct: 122 AKQVVFGSLTILFFLLAARDFTGSELIGMIAGFEGIFCGASAIYFAMAQVLNQEYGRVIL 181 Query: 183 PIGE 186 PIGE Sbjct: 182 PIGE 185 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: 246 Number of extensions: 18 Number of successful extensions: 1 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: 188 Length adjustment: 20 Effective length of query: 168 Effective length of database: 168 Effective search space: 28224 Effective search space used: 28224 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