Align GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate PfGW456L13_2615 Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)
Query= TCDB::G3LHZ1 (273 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2615 Length = 266 Score = 444 bits (1142), Expect = e-130 Identities = 213/261 (81%), Positives = 236/261 (90%), Gaps = 1/261 (0%) Query: 14 LVPT-IYIIFLILPIYWLINMSFKENSEITGAFSLWPTNPTLRNYTVIFTDPSWYNGYIN 72 L+P IYI+FL++PIYWL+NMSFK NSEI G +L+P + TL NY VIFTDPSWY GYIN Sbjct: 6 LIPLLIYILFLLVPIYWLLNMSFKSNSEILGGLTLFPQDFTLANYKVIFTDPSWYTGYIN 65 Query: 73 SIIYVVMNTVISVAAALPAAYAFSRYRFLGDKHLFFWLLTNRMAPPAVFALPFFQLYSAF 132 S YV +NT+IS+ ALPAAYAFSRYRFLGDKHLFFWLLTNRMAPPAVF LPFFQLYS+ Sbjct: 66 SAYYVSLNTIISLTVALPAAYAFSRYRFLGDKHLFFWLLTNRMAPPAVFLLPFFQLYSSI 125 Query: 133 GLIDTHIAVALAHCLFNVPLAVWILEGFMSGVPKEIDETAYIDGYSFPRFFIKIFIPLIA 192 GL DTHIAVALAHCLFNVPLAVWILEGFMSGVPKEIDETAYIDGYSFP+FF+KIFIPLI Sbjct: 126 GLFDTHIAVALAHCLFNVPLAVWILEGFMSGVPKEIDETAYIDGYSFPKFFVKIFIPLIG 185 Query: 193 SGVGVAGFFCFMFSWVELLLARTLTTTAAKPISAIMTRTVSASGMDWGVLAAAGVLTIIP 252 SG+GV FFCFMFSWVELLLARTLT+ AKPI+A+MTRTVSASG+DWGVLAAAGVLTI+P Sbjct: 186 SGIGVTAFFCFMFSWVELLLARTLTSVNAKPIAAVMTRTVSASGIDWGVLAAAGVLTILP 245 Query: 253 GALVIYFVRNYIAKGFALGRV 273 G LVI+FVRN++AKGFALGRV Sbjct: 246 GMLVIWFVRNHVAKGFALGRV 266 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: 387 Number of extensions: 7 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: 266 Length adjustment: 25 Effective length of query: 248 Effective length of database: 241 Effective search space: 59768 Effective search space used: 59768 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 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