Align GlpP, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 3608006 Dshi_1414 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::G3LHZ0 (288 letters) >FitnessBrowser__Dino:3608006 Length = 343 Score = 89.4 bits (220), Expect = 1e-22 Identities = 74/242 (30%), Positives = 126/242 (52%), Gaps = 24/242 (9%) Query: 46 FWAGTDW---FVQTLHSDRFWESLQRNLLFSFIILALEIPLGIFIALN---MPKSGPGVP 99 FW +D F + ++ F+++L L ++FI+ L I LG IA+ +P+ G P Sbjct: 95 FWRSSDSLGAFARQVYGLPFYKALTFTLAYTFIVTPLIIALGFLIAVAVNALPRLLKG-P 153 Query: 100 VCLVLMALPLLIPWNVVGTI---WQVFGRVDIGLLGHTLEAI--GLDYNYVRDPIDAWVT 154 V + LP++I +VG++ W + R G++G TL+ I D + P+ W+T Sbjct: 154 VIFTSL-LPMIIT-PLVGSLILFWMIDSR---GVIGKTLQFIFEDPDLSLKASPMLTWIT 208 Query: 155 VIVMDVWHWTSLVVLLCYAGLVSIPDAYYQAAKIDGASRWSVFRYIQLPKMKRVLLIAVL 214 ++V VW ++ YAGL ++P ++A IDGA+RW R++ LP + ++ L Sbjct: 209 LMVYGVWSSAPFAFVVFYAGLQTVPQDTLESAMIDGATRWQRIRFVVLPYLMPLVTFIAL 268 Query: 215 LRFMDSFMIYTEPFVVTGGGPGNSTTFLSI---DLVKMAVGQFDLGPAAAMSIIYFLIIL 271 ++ MD+F ++ EP +V N+T+ I DL V F G AAA S++ L + Sbjct: 269 IQLMDNFRVF-EP-IVGFNAEANATSLSWIIYNDLRGSEVALF--GSAAATSMLTILGVA 324 Query: 272 LL 273 +L Sbjct: 325 IL 326 Lambda K H 0.329 0.143 0.464 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: 283 Number of extensions: 11 Number of successful extensions: 2 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: 288 Length of database: 343 Length adjustment: 27 Effective length of query: 261 Effective length of database: 316 Effective search space: 82476 Effective search space used: 82476 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: 48 (23.1 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