Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 224 bits (572), Expect = 2e-63 Identities = 124/296 (41%), Positives = 188/296 (63%), Gaps = 5/296 (1%) Query: 39 LVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILSISAV 98 L+++CI +++F N+ + +Q SIN ++A GMT VILTGGIDLSVGS+++++ Sbjct: 43 LLVVCIVMVFASDSFLSGANIENVLRQVSINAIIAVGMTCVILTGGIDLSVGSVMALAGT 102 Query: 99 VA--MLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLARL 156 +A ++V+ M + L++ A+ GL FG NG VAF +PP IVTL T+ RGLA + Sbjct: 103 LAAGLMVAGMNAVAALAIGIAV--GLGFGAANGFFVAFAGMPPIIVTLATMGIARGLALI 160 Query: 157 VGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAE 216 I +F G+G++LGV V+I + ++W +L R G +YA+GGN + Sbjct: 161 YTGGYPIDGLPDWVSFFGSGKILGVQAPVVIMAVIYVIAWVLLERMPFGRYVYAIGGNEQ 220 Query: 217 AARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGT 276 A RLSG++V V L VY ++GL + ++ +ARL + G +ELDAIAAV++GGT Sbjct: 221 ATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQP-NAGVGFELDAIAAVVMGGT 279 Query: 277 SFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRK 332 S GG GSI+GTL+GAL++ VL+NGL ++GV+ Q +IKG +I+ A+ + RRK Sbjct: 280 SISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGGIILLAIYISRDRRK 335 Lambda K H 0.325 0.141 0.409 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: 365 Number of extensions: 21 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: 337 Length of database: 335 Length adjustment: 28 Effective length of query: 309 Effective length of database: 307 Effective search space: 94863 Effective search space used: 94863 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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