Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate YP_004140698.1 Mesci_1489 inner-membrane translocator
Query= TCDB::O05177 (398 letters) >NCBI__GCF_000185905.1:YP_004140698.1 Length = 332 Score = 136 bits (342), Expect = 1e-36 Identities = 108/382 (28%), Positives = 177/382 (46%), Gaps = 76/382 (19%) Query: 20 IRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGH 79 +R+ GML L+ + FQF L NL + Q+S +++A GM VI+ G Sbjct: 21 LRTAFAALGMLPVLILLAAGFQFLNPRFLTE-TNLLIVTQQSSINIVLAAGMTFVILTGG 79 Query: 80 IDLSVGSIVAFVGAIAAILTV--QWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFI 137 IDLSVG+I+A +A I+++ WG+ +G +P+ I Sbjct: 80 IDLSVGAILAASAMVAVIVSLVPDWGL---------------LG-----------VPAAI 113 Query: 138 VTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVA 197 + G + GL + + + PF +++ G L + G+ L Sbjct: 114 LVGLGFGLINGLLIAYI---KLPPF-----IVTLGSLTAVRGVARLL------------- 152 Query: 198 LFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLI 257 G D F + + + +G++ G+P ++I+ L ++ Sbjct: 153 ---------------GQDTTVFNSDLPFDFIGNGSLF----------GIPWLVIIALSVV 187 Query: 258 ALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLN 317 L V +RT +G +YA+GGN +A +L+GI + + G+LAGL G + A RL Sbjct: 188 VLSWLVLKRTVLGTWIYAVGGNAEAARLTGIKVPLVLLFVYGVSGLLAGLGGAMSAARLY 247 Query: 318 SATP-KAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQ 376 +A + G +ELD IAA +GG S GGVG I G +IG I+ V++NG+ + G+ +Q Sbjct: 248 AANGLQLGQSYELDAIAAVILGGTSFVGGVGSIWGTLIGGLIIAVLSNGLILAGVSDIWQ 307 Query: 377 QMVKGLVLLAAVFFDVYNKNKG 398 ++KGLV++ AV D Y G Sbjct: 308 YIIKGLVIIVAVALDRYRLQAG 329 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: 477 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 398 Length of database: 332 Length adjustment: 29 Effective length of query: 369 Effective length of database: 303 Effective search space: 111807 Effective search space used: 111807 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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