Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate 16257 b2148 beta-methylgalactoside transporter inner membrane component (NCBI)
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Keio:16257 Length = 336 Score = 198 bits (504), Expect = 1e-55 Identities = 121/324 (37%), Positives = 186/324 (57%), Gaps = 22/324 (6%) Query: 30 LRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSV 89 L+ G+ VL++L F NLS I Q+S+ +++A G+ +I+T G DLS Sbjct: 13 LKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSA 72 Query: 90 GSILSISAVVAMLV--------SLMPQLGMLSVPAALLC----GLLFGIVNGALVAFMKL 137 G + ++AVVA + + P++ + + +L G + G++NG ++A++ + Sbjct: 73 GRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNV 132 Query: 138 PPFIVTLGTLTAVRGLARLVGN---DSTIYNPDIGFAFIGNGEV-LG---VPWLVIIAFA 190 PFI TLGT+ V G+ L + S I D GF+ G V LG + ++ A Sbjct: 133 TPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALI 192 Query: 191 VVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSAR 250 VA W + +T G I+A+GGN EAA++SG+ V + LL +YA+SG+ GG++ + R Sbjct: 193 AVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGR 252 Query: 251 LYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDI 310 + +A LG YELDAIAA ++GG SF GG G+++G + G +I V++ GL +GV+ Sbjct: 253 IGSATN-NLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPY 311 Query: 311 WQYIIKGLVIIGAVALDS--YRRK 332 WQYIIKG +II AVALDS Y RK Sbjct: 312 WQYIIKGAIIIFAVALDSLKYARK 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: 320 Number of extensions: 18 Number of successful extensions: 5 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: 336 Length adjustment: 28 Effective length of query: 309 Effective length of database: 308 Effective search space: 95172 Effective search space used: 95172 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