Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate 18114 b4086 D-allose transporter subunit (NCBI)
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Keio:18114 Length = 326 Score = 195 bits (495), Expect = 2e-54 Identities = 117/291 (40%), Positives = 170/291 (58%), Gaps = 6/291 (2%) Query: 40 VLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILSISAVV 99 +++ I S+ E F N++ I Q+S+ +++ G F IL GIDLSVG+IL++S +V Sbjct: 34 IIVAIFGSLSPEYFLTTNNITQIFVQSSVTVLIGMGEFFAILVAGIDLSVGAILALSGMV 93 Query: 100 A---MLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLARL 156 ML + P L + +L G G +NG LV + L PFI+TLGT RG+ + Sbjct: 94 TAKLMLAGVDPFLAAMI--GGVLVGGALGAINGCLVNWTGLHPFIITLGTNAIFRGITLV 151 Query: 157 VGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAE 216 + + +++Y F V+G+P VI + V + WF+ R LG IYA+GGN Sbjct: 152 ISDANSVYGFSFDFVNFFAASVIGIPVPVIFSLIVALILWFLTTRMRLGRNIYALGGNKN 211 Query: 217 AARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGT 276 +A SGI V +L V+ +SG+ AGL GV+S+ARL AA L G +E AIA+ I+GGT Sbjct: 212 SAFYSGIDVKFHILVVFIISGVCAGLAGVVSTARLGAAEPL-AGMGFETYAIASAIIGGT 270 Query: 277 SFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALD 327 SF GG G I ++G LII ++NGL +L V +Q ++ G +II AVALD Sbjct: 271 SFFGGKGRIFSVVIGGLIIGTINNGLNILQVQTYYQLVVMGGLIIAAVALD 321 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: 368 Number of extensions: 15 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: 326 Length adjustment: 28 Effective length of query: 309 Effective length of database: 298 Effective search space: 92082 Effective search space used: 92082 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