Align Acetate permease A; Monocarboxylate transporter acpA (characterized)
to candidate BPHYT_RS27785 BPHYT_RS27785 hypothetical protein
Query= SwissProt::Q5B2K4 (298 letters) >FitnessBrowser__BFirm:BPHYT_RS27785 Length = 201 Score = 109 bits (272), Expect = 6e-29 Identities = 72/203 (35%), Positives = 104/203 (51%), Gaps = 31/203 (15%) Query: 81 KFANPAPLGLSAFALTTFVLSCINMGARDITHPNIVIALAFGYGGLVQLLAGMWEMAVGN 140 K NPA LGL+ FALTT++LS IN G + +V+A+AF YGG Q++AG+ E+ GN Sbjct: 4 KAPNPASLGLAGFALTTWLLSMINAGWFNGESMGMVLAVAFAYGGTAQMIAGLMEIPRGN 63 Query: 141 TFGATALSSYGGFWIAFAIVLTPGGFNIQTALTAENGDEAMFYNSFGLFLMGWFIFTTIM 200 FGATA SYG FW + A+ + N+ A G +L W +FT M Sbjct: 64 AFGATAFLSYGAFWWSLALFVLFLHGNVPAAF-------------IGWYLFLWGMFTLYM 110 Query: 201 LFCTLRSTVAFFLLFLFLDLAFLLL------GVGYIQRDDAGQPNPPVIKAGGFFGLLAA 254 T R+ A L+FL L L F +L G+ ++ AGG+ GL+ A Sbjct: 111 WVATWRAARALQLVFLSLWLTFFVLAASEWTGLAWLHH------------AGGYLGLVTA 158 Query: 255 FAAWYNALAGIADSSNSFFIIPV 277 A+Y + A I + ++ ++PV Sbjct: 159 LLAFYLSAAEIINETHGRVVLPV 181 Lambda K H 0.324 0.139 0.436 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: 184 Number of extensions: 12 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: 298 Length of database: 201 Length adjustment: 24 Effective length of query: 274 Effective length of database: 177 Effective search space: 48498 Effective search space used: 48498 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 46 (22.3 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