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 PP_2761 PP_2761 putative Ribose ABC transporter, permease protein
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__Putida:PP_2761 Length = 328 Score = 105 bits (262), Expect = 2e-27 Identities = 91/304 (29%), Positives = 145/304 (47%), Gaps = 16/304 (5%) Query: 15 IIVVMIVVFSTRAADFATPGNLAGIF-NDTSILIILALAQMTVILTKSIDLSVAANLAFT 73 + +++ F+ +A F T GNL+ + N+ +L I+A+ I IDLSV L F+ Sbjct: 29 LFAAVLLFFALKAPGFLTVGNLSSLLLNNFVLLAIVAIGMTYAIAAGGIDLSVGTALDFS 88 Query: 74 GMA-IAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRGM 132 + + ++NA L V I ++ G+ G N L+ L I P + TLGTL I + Sbjct: 89 ALTFVLLLNAG---FGLYVAIPGGLLAGSLAGLFNAGLIAGLRISPFLATLGTLFIGSSV 145 Query: 133 AFVLS-GGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAYA 191 +LS GG + L+ R +LG+P+ + ++ ++ V+L + GR Sbjct: 146 QKLLSEGGQPIYLEAQVRSGLATER--MLGVPLPLLLVALLALVYGVVLARGRLGREIIV 203 Query: 192 TGGNPTAAVYAGIDTGWTKFLAFVLS---GALAGLASYLWVSRYAVAYVDIANGFELDSV 248 G P A Y+G+ L F+ S ALAG+ V+ YA N F ++++ Sbjct: 204 LGSQPLVARYSGLAQRRIAALVFIASAFASALAGILLPATVNAYAPM---SGNAFLMNAI 260 Query: 249 AACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVI--ILAVAF 306 A IG +V GT+LG LFL V N L +IG + F Q +G +I +L +F Sbjct: 261 GAVFIGATLSLHNRVNVPGTLLGVLFLNVTANGLLLIGWNFFWQQVATGVLILSVLLFSF 320 Query: 307 NARR 310 +RR Sbjct: 321 ASRR 324 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: 250 Number of extensions: 12 Number of successful extensions: 1 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: 328 Length adjustment: 28 Effective length of query: 305 Effective length of database: 300 Effective search space: 91500 Effective search space used: 91500 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