Align RhaP, 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 WP_085121058.1 B9O00_RS01465 ABC transporter permease
Query= TCDB::Q7BSH3 (333 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 165 bits (417), Expect = 2e-45 Identities = 110/318 (34%), Positives = 173/318 (54%), Gaps = 13/318 (4%) Query: 3 RLIRKRETLLFL----IIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVIL 58 RL+++ T L L + +V+ V S + F T N+ I + + ++ IL++ VIL Sbjct: 23 RLLKQLATSLELRMLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVIL 82 Query: 59 TKSIDLSVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPP 118 T IDLSV + +G+ + + A D P+ V IL+ V+ GA +G ++G L+ + Sbjct: 83 TGGIDLSVGSVAGLSGIVLGL---ALKDYPIPVAILLGVLTGAGVGLVSGILIGYFRLAA 139 Query: 119 IVVTLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYV 178 VVTLG + I R +A++ SG ++ S+ T V G+P +L + Sbjct: 140 FVVTLGMMAIGRSLAYIFSGQTAISGFPSD--LSSIVYTDVFGIPTNVLFLGFAYLLAWG 197 Query: 179 LLRYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVD 238 L YT+ GR+ YA G N AA AG+ + L +V+SGALA +A V++ Sbjct: 198 YLTYTKGGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDPL 257 Query: 239 IANGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGT 298 NG ELD++AA VIGG S+ GG GS+ GT++G L + +I+N L ++G+SPF Q + G+ Sbjct: 258 TGNGMELDAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGS 317 Query: 299 VIILAV----AFNARRER 312 +II+A+ AR ER Sbjct: 318 IIIMALLVERLVRARSER 335 Lambda K H 0.328 0.141 0.413 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: 290 Number of extensions: 25 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: 1 Length of query: 333 Length of database: 335 Length adjustment: 28 Effective length of query: 305 Effective length of database: 307 Effective search space: 93635 Effective search space used: 93635 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 Apr 09 2024. 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