Align GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF2207 HP15_2161 sugar ABC transporter, permease protein
Query= TCDB::G3LHZ1 (273 letters) >FitnessBrowser__Marino:GFF2207 Length = 269 Score = 427 bits (1097), Expect = e-124 Identities = 200/257 (77%), Positives = 227/257 (88%) Query: 17 TIYIIFLILPIYWLINMSFKENSEITGAFSLWPTNPTLRNYTVIFTDPSWYNGYINSIIY 76 T++I+ L+ PIYWL+NMSFK N EI G +LWP N TL NY VIFTDPSWYNGYINS+IY Sbjct: 13 TLFILLLLTPIYWLLNMSFKTNQEILGGLTLWPQNFTLDNYAVIFTDPSWYNGYINSMIY 72 Query: 77 VVMNTVISVAAALPAAYAFSRYRFLGDKHLFFWLLTNRMAPPAVFALPFFQLYSAFGLID 136 V +N VI++ ALPAAYAFSRY+FLGDKHLFFWLL+NRMAPPAVF LPFFQLYS+ GL D Sbjct: 73 VSINVVITLLVALPAAYAFSRYKFLGDKHLFFWLLSNRMAPPAVFLLPFFQLYSSIGLFD 132 Query: 137 THIAVALAHCLFNVPLAVWILEGFMSGVPKEIDETAYIDGYSFPRFFIKIFIPLIASGVG 196 THIAVALAHCLFNVPLAVWILEGFMSGVP+E DE AYIDGYSFP+FF+K+F+P+I SG+G Sbjct: 133 THIAVALAHCLFNVPLAVWILEGFMSGVPREYDEMAYIDGYSFPKFFVKVFLPMIRSGIG 192 Query: 197 VAGFFCFMFSWVELLLARTLTTTAAKPISAIMTRTVSASGMDWGVLAAAGVLTIIPGALV 256 V FF FMFSWVELLLARTLT+ A+PI AIMTRT+ ASG+DWGVLAAAG LTIIPG LV Sbjct: 193 VTAFFAFMFSWVELLLARTLTSVDAQPIGAIMTRTIGASGIDWGVLAAAGSLTIIPGLLV 252 Query: 257 IYFVRNYIAKGFALGRV 273 I+FVRN++AKGFALGRV Sbjct: 253 IWFVRNHVAKGFALGRV 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: 359 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: 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