Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate SM_b20714 SM_b20714 sugar uptake ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Smeli:SM_b20714 Length = 341 Score = 209 bits (532), Expect = 8e-59 Identities = 124/323 (38%), Positives = 188/323 (58%), Gaps = 24/323 (7%) Query: 33 LGMLPVLVLLCIGFSVLTENFAGW------QNLSIIAQQASINMVLAAGMTFVILTGGID 86 L + VL+ + + + VL F G Q L+I+ Q S+ ++A G+T VI+TGGID Sbjct: 25 LNIFLVLIGIALVYEVLGWLFVGQSFLMNSQRLTIMILQVSVIGIIAVGVTQVIITGGID 84 Query: 87 LSVGSILSISAVVAMLVS--------LMPQL----GMLSVPAALLCGLLFGIVNGALVAF 134 LS GS++ ++A+++ V+ L P L ++ + + GLL G +NG L+A Sbjct: 85 LSSGSVVGMTAMISASVAQASTWPRALYPSLTDLPAIVPIGLGVGIGLLAGFINGQLIAR 144 Query: 135 MKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAV 194 K+PPFI TLG + + RG+++ + F FIG G W VI+ V + Sbjct: 145 TKIPPFIATLGMMVSARGVSKWYTKGQPVSGLTEQFNFIGTGI-----WPVIVFLVVALI 199 Query: 195 SWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAA 254 LR T G YA+G N +AAR+SGI V L+ VYA++G+LAGL GV+++AR A Sbjct: 200 FHIALRYTRYGKFTYAIGANVQAARVSGINVEAHLVKVYAIAGMLAGLAGVVTAARAQTA 259 Query: 255 NGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYI 314 +G YELDAIAA ++GGTS GG G + GT++G +I+ V+++G L V +Q I Sbjct: 260 QA-GMGVMYELDAIAATVIGGTSLTGGVGRVTGTVIGTVILGVMTSGFTFLRVDAYYQEI 318 Query: 315 IKGLVIIGAVALDSYRRKGSART 337 +KG++I+ AV +D YR+KG +T Sbjct: 319 VKGIIIVAAVVVDVYRQKGRKKT 341 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: 360 Number of extensions: 20 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: 341 Length adjustment: 28 Effective length of query: 309 Effective length of database: 313 Effective search space: 96717 Effective search space used: 96717 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