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 N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 125 bits (314), Expect = 2e-33 Identities = 95/304 (31%), Positives = 153/304 (50%), Gaps = 10/304 (3%) Query: 6 RKRETLLFLIIVVMIVVFSTRAA----DFATPGNLAGIFNDTSILIILALAQMTVILTKS 61 R+R + L+ +V+ V + F TP + D + L I+A+ VIL Sbjct: 20 RRRAQVPLLVTLVLFVAMAGAGGVLYHGFLTPQVFLNLLIDNAFLCIVAVGMTFVILAGG 79 Query: 62 IDLSVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVV 121 IDLSV A +AF+ + +A + H PL + L+ + +G GA G L+ + P VV Sbjct: 80 IDLSVGAVVAFSTVLLAELVQRHGWPPLAAIALV-LAVGTGFGAGMGVLIQRFRLQPFVV 138 Query: 122 TLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLS---WVGIIIVILMYV 178 TL + + RG+A ++S + ++ Q ++ R P+ G +LS V + +V + Sbjct: 139 TLAGMFLARGVATLISVDS-IDIDQPWLASVANLRLPLGGGSMLSVGALVALAVVAAGAL 197 Query: 179 LLRYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVD 238 L + FGR+ YA GG+ ++A G+ T + LSG A LA ++ Y Sbjct: 198 LAGASSFGRTVYAIGGSESSARLMGLPVDATVVRVYALSGFCAALAGVVYTLYMLSGYSQ 257 Query: 239 IANGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIG-ISPFTQMAISG 297 A G ELD++AA VIGG +AGG G V GT+LG L LG+I+ + G +S + + G Sbjct: 258 HALGLELDAIAAVVIGGTVLAGGSGYVLGTLLGVLVLGLIQTLIVFDGELSSWWTRIVIG 317 Query: 298 TVII 301 +++ Sbjct: 318 ALLL 321 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: 297 Number of extensions: 17 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: 333 Length of database: 337 Length adjustment: 28 Effective length of query: 305 Effective length of database: 309 Effective search space: 94245 Effective search space used: 94245 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