Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate SM_b20893 SM_b20893 sugar uptake ABC transporter permease
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Smeli:SM_b20893 Length = 404 Score = 564 bits (1453), Expect = e-165 Identities = 285/398 (71%), Positives = 334/398 (83%), Gaps = 6/398 (1%) Query: 7 TNEESNVISVGSYIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVI 66 T+ E+ S+G Y+R+NIREYG+L+ALV IM+FFQF T G+LFRPVN+TNL+LQNSFIVI Sbjct: 5 TSTETTKPSIGDYLRNNIREYGLLVALVIIMLFFQFVTNGVLFRPVNITNLVLQNSFIVI 64 Query: 67 MALGMLLVIVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGY 126 MALGMLL+IVAGHIDLSVGSIVAF+GAI+AI+ V+WG+ F+ CL++GGI+GAAQGY Sbjct: 65 MALGMLLIIVAGHIDLSVGSIVAFIGAISAIMLVKWGLPAFVVIPACLIVGGIMGAAQGY 124 Query: 127 WIAYHRIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDI-----GGIE 181 W+AY +IPSFIVTLAGMLVFRG+T VLGG+ IGPFP DFQ++STGF+PD E Sbjct: 125 WVAYQKIPSFIVTLAGMLVFRGMTYVVLGGRPIGPFPKDFQILSTGFVPDFLYFLSPSPE 184 Query: 182 GLNTTSMILTVLITVALFYLAW-RRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQL 240 + ++ VL+ V A R R +N +HG + EPF FF +Q +IS LFLG+QL Sbjct: 185 TIKNMVALVAVLLLVGYAIFAGVRNRRINEQHGTENEPFVFFAIQMAVISLVALFLGFQL 244 Query: 241 STYRGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVN 300 STYRGLPNVL+VM VLIA+Y+FVT R+TIGRR+YAMGGNEKATKLSGINTERL+F FVN Sbjct: 245 STYRGLPNVLVVMGVLIAVYTFVTTRSTIGRRIYAMGGNEKATKLSGINTERLTFYAFVN 304 Query: 301 MGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMG 360 MG LA LAGMII RLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMG Sbjct: 305 MGALAALAGMIITARLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMG 364 Query: 361 VMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDVYNKNKG 398 VMNNGMSI+G+GID+QQ++KGLVLLAAVFFDVYNKNKG Sbjct: 365 VMNNGMSIMGIGIDYQQLIKGLVLLAAVFFDVYNKNKG 402 Lambda K H 0.329 0.145 0.422 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: 747 Number of extensions: 40 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: 398 Length of database: 404 Length adjustment: 31 Effective length of query: 367 Effective length of database: 373 Effective search space: 136891 Effective search space used: 136891 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: 50 (23.9 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