Align RhaS, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate H281DRAFT_02713 H281DRAFT_02713 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__Burk376:H281DRAFT_02713 Length = 313 Score = 124 bits (310), Expect = 4e-33 Identities = 88/294 (29%), Positives = 150/294 (51%), Gaps = 13/294 (4%) Query: 1 MKLAKTLALGVALAVAMMAGTAS----AKDIKIGLVVKSLGNGFFDAANKGAQEAAKELG 56 MKL + +A+A G + AKDI + ++ K + FFD NKGA+ AA + Sbjct: 1 MKLTQRFTASALVALAASVGATAHAKDAKDISVAVIPK-VAVPFFDDCNKGAKTAAGK-A 58 Query: 57 GVEVIYTGPTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWD 116 GV+ + P +T Q+++I LI++ VD IA+S N+P ++ +K+A Q GIKV+++D Sbjct: 59 GVKYQWVVPQNTQGSTQVQIIEDLISRHVDGIAISVNEPKSVESVMKRAEQSGIKVLTYD 118 Query: 117 SGVAPEGRILQLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKK 176 S GR + + ++ + M T+ K G+G+ AI++ + N N I +KK Sbjct: 119 SDSPRSGRSMYIGTNNEQAGATMAETMGK--ALNGQGEVAIITGQLGAVNLNERIAGIKK 176 Query: 177 QLKDFPGLNLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDK-- 234 L +PG+ +V T DD + E L+++P +K I + VG A +KV+ K Sbjct: 177 GLAKYPGIKIVETQGTDDDLARGVSVVETTLRAHPQLKGIFGVSQVGGPAVAKVLNTKEF 236 Query: 235 -GLVGKVYVTGL-GLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGE 286 + GK+ V LP + G +K G + + P+ +G A + ++G+ Sbjct: 237 GTMKGKLEVLAFDDLPDTLKG-LKEGYIQGIMVQRPVTMGSLAVEHLVAQIQGQ 289 Lambda K H 0.313 0.131 0.365 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: 238 Number of extensions: 14 Number of successful extensions: 3 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: 331 Length of database: 313 Length adjustment: 28 Effective length of query: 303 Effective length of database: 285 Effective search space: 86355 Effective search space used: 86355 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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