Align GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate BPHYT_RS33285 BPHYT_RS33285 sugar ABC transporter permease
Query= TCDB::G3LHZ1 (273 letters) >FitnessBrowser__BFirm:BPHYT_RS33285 Length = 269 Score = 434 bits (1115), Expect = e-126 Identities = 205/259 (79%), Positives = 233/259 (89%) Query: 15 VPTIYIIFLILPIYWLINMSFKENSEITGAFSLWPTNPTLRNYTVIFTDPSWYNGYINSI 74 V T+YI+F ++P+YW++++S + N E AF++WP + T NY VIFTDPSWY GYINSI Sbjct: 11 VLTVYILFALIPLYWMLSISLRTNEETMSAFAIWPHHVTFDNYKVIFTDPSWYWGYINSI 70 Query: 75 IYVVMNTVISVAAALPAAYAFSRYRFLGDKHLFFWLLTNRMAPPAVFALPFFQLYSAFGL 134 IYV+MNTV+SV ALPAAYAFSRYRFLGDKH+FFWLLTNRM PPAVF LPFFQLYS+ GL Sbjct: 71 IYVLMNTVMSVLVALPAAYAFSRYRFLGDKHMFFWLLTNRMTPPAVFLLPFFQLYSSVGL 130 Query: 135 IDTHIAVALAHCLFNVPLAVWILEGFMSGVPKEIDETAYIDGYSFPRFFIKIFIPLIASG 194 +DT+IAVALAH LFNVPLAVWILEGFMSGVP+EIDETAYIDGY+FP FFIKIF+PLI SG Sbjct: 131 MDTYIAVALAHMLFNVPLAVWILEGFMSGVPREIDETAYIDGYTFPAFFIKIFLPLIKSG 190 Query: 195 VGVAGFFCFMFSWVELLLARTLTTTAAKPISAIMTRTVSASGMDWGVLAAAGVLTIIPGA 254 VGV FFCFMFSWVELLLARTLTT AKPI+A+MTRTVSA+GMDWGVL+AAGVLTI+PGA Sbjct: 191 VGVTAFFCFMFSWVELLLARTLTTVNAKPIAAVMTRTVSAAGMDWGVLSAAGVLTIVPGA 250 Query: 255 LVIYFVRNYIAKGFALGRV 273 LVIYFVRNYIAKGFA+GRV Sbjct: 251 LVIYFVRNYIAKGFAMGRV 269 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: 396 Number of extensions: 11 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: 269 Length adjustment: 25 Effective length of query: 248 Effective length of database: 244 Effective search space: 60512 Effective search space used: 60512 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