Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate H281DRAFT_00427 H281DRAFT_00427 monosaccharide ABC transporter membrane protein, CUT2 family
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Burk376:H281DRAFT_00427 Length = 341 Score = 159 bits (402), Expect = 1e-43 Identities = 107/366 (29%), Positives = 180/366 (49%), Gaps = 62/366 (16%) Query: 32 ALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIVAFV 91 +L+ ++VFF F + + + N+ ++ + ++A+ VI+ G IDLSVG+++ F Sbjct: 37 SLILLLVFFSFASPAFM-QMDNILGILQATAVNGVLAIASTFVIITGGIDLSVGTLMTFT 95 Query: 92 GAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRGLTL 151 I + W + +L + + G I G T++G L + Sbjct: 96 AVICGVFLTYWHLPMWLGVIAAIGTGAICG-----------------TISGTLTAK---- 134 Query: 152 FVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRVVNVK 211 I PF + + G + + G+ L V +++ Sbjct: 135 -----MKIPPF-----IATLGMMLLLKGLS--------LVVSADKPIYFT---------- 166 Query: 212 HGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRTTIGR 271 D E F + I Q+ LI GY + + +PN ++++ L + S RT +GR Sbjct: 167 ---DTENF-YMISQDSLI-------GYLVPSLP-IPNAVLILFFLAIVSSVTLNRTALGR 214 Query: 272 RVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFELDV 331 +A+G NE+A +LSG+N +R + G + G+AG++IA+RLNSA P G G+EL+ Sbjct: 215 YTFALGSNEEAVRLSGVNVDRWKIAIYGLGGAICGIAGLLIASRLNSAQPALGQGYELEA 274 Query: 332 IAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAVFFD 391 IAA IGG S SGG G I G +IGAFIM V+ NG+ I+ + ++Q +V GL+++ AV+ D Sbjct: 275 IAAVVIGGTSLSGGSGTILGTIIGAFIMSVLTNGLRIMSVAQEWQIVVTGLIIILAVYAD 334 Query: 392 VYNKNK 397 + + K Sbjct: 335 ILRRRK 340 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: 431 Number of extensions: 27 Number of successful extensions: 2 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: 341 Length adjustment: 30 Effective length of query: 368 Effective length of database: 311 Effective search space: 114448 Effective search space used: 114448 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 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