Align GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate AZOBR_RS25890 AZOBR_RS25890 sugar ABC transporter permease
Query= TCDB::G3LHZ1 (273 letters) >FitnessBrowser__azobra:AZOBR_RS25890 Length = 265 Score = 433 bits (1114), Expect = e-126 Identities = 205/260 (78%), Positives = 232/260 (89%) Query: 14 LVPTIYIIFLILPIYWLINMSFKENSEITGAFSLWPTNPTLRNYTVIFTDPSWYNGYINS 73 +V T+YI+FL+LPIYWL+NMS K N+EI +LWP T NY IFTD SWY+GY+NS Sbjct: 6 IVLTLYILFLMLPIYWLVNMSLKTNTEIVSGLTLWPHTLTFENYRRIFTDSSWYSGYLNS 65 Query: 74 IIYVVMNTVISVAAALPAAYAFSRYRFLGDKHLFFWLLTNRMAPPAVFALPFFQLYSAFG 133 + YV +NTV+S+A ALPAAYAFSRYRF+GDKHLFFWLL+NRMAP AVFALPFF LYSA G Sbjct: 66 LQYVALNTVLSIALALPAAYAFSRYRFVGDKHLFFWLLSNRMAPAAVFALPFFNLYSAIG 125 Query: 134 LIDTHIAVALAHCLFNVPLAVWILEGFMSGVPKEIDETAYIDGYSFPRFFIKIFIPLIAS 193 L DT +AVALAHCLFNVPLAVWILEGFMSGVP+EIDETAY+DGYSFPRFF+KIF+PL+AS Sbjct: 126 LFDTPLAVALAHCLFNVPLAVWILEGFMSGVPREIDETAYLDGYSFPRFFVKIFMPLVAS 185 Query: 194 GVGVAGFFCFMFSWVELLLARTLTTTAAKPISAIMTRTVSASGMDWGVLAAAGVLTIIPG 253 G+GV FFCFMFSWVELLLARTLT+ AKPI+A MTRTVSASGMDWG+LAAAGVLTI+PG Sbjct: 186 GIGVTAFFCFMFSWVELLLARTLTSVDAKPIAATMTRTVSASGMDWGLLAAAGVLTILPG 245 Query: 254 ALVIYFVRNYIAKGFALGRV 273 ALVI+FVRNYIAKGFALGRV Sbjct: 246 ALVIWFVRNYIAKGFALGRV 265 Lambda K H 0.330 0.142 0.456 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: 377 Number of extensions: 9 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: 273 Length of database: 265 Length adjustment: 25 Effective length of query: 248 Effective length of database: 240 Effective search space: 59520 Effective search space used: 59520 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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