Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate PP_2761 PP_2761 putative Ribose ABC transporter, permease protein
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Putida:PP_2761 Length = 328 Score = 137 bits (345), Expect = 4e-37 Identities = 100/325 (30%), Positives = 167/325 (51%), Gaps = 7/325 (2%) Query: 11 STGAPLPAGTLGRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLS-IIAQQASIN 69 S AP PAG G L+ + LR L M + + + F++ F NLS ++ + Sbjct: 4 SLSAPQPAGLTG-LSGRALLR-LVMPTLFAAVLLFFALKAPGFLTVGNLSSLLLNNFVLL 61 Query: 70 MVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGM-LSVPAALLCGLLFGIVN 128 ++A GMT+ I GGIDLSVG+ L SA+ +L+ L G+ +++P LL G L G+ N Sbjct: 62 AIVAIGMTYAIAAGGIDLSVGTALDFSALTFVLL-LNAGFGLYVAIPGGLLAGSLAGLFN 120 Query: 129 GALVAFMKLPPFIVTLGTLTAVRGLARLVGNDST-IYNPDIGFAFIGNGEVLGVPWLVII 187 L+A +++ PF+ TLGTL + +L+ IY + + +LGVP +++ Sbjct: 121 AGLIAGLRISPFLATLGTLFIGSSVQKLLSEGGQPIYLEAQVRSGLATERMLGVPLPLLL 180 Query: 188 AFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMS 247 + V VL R LG +I +G AR SG+ + V+ S + L G++ Sbjct: 181 VALLALVYGVVLARGRLGREIIVLGSQPLVARYSGLAQRRIAALVFIASAFASALAGILL 240 Query: 248 SARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGV 307 A + A + G ++ ++AI AV +G T + ++ GTL+G L + V +NGL+L+G Sbjct: 241 PATVNAYAPMS-GNAFLMNAIGAVFIGATLSLHNRVNVPGTLLGVLFLNVTANGLLLIGW 299 Query: 308 SDIWQYIIKGLVIIGAVALDSYRRK 332 + WQ + G++I+ + R+ Sbjct: 300 NFFWQQVATGVLILSVLLFSFASRR 324 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: 331 Number of extensions: 22 Number of successful extensions: 4 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: 328 Length adjustment: 28 Effective length of query: 309 Effective length of database: 300 Effective search space: 92700 Effective search space used: 92700 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