Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate SM_b21375 SM_b21375 sugar uptake ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Smeli:SM_b21375 Length = 320 Score = 212 bits (540), Expect = 9e-60 Identities = 122/294 (41%), Positives = 176/294 (59%), Gaps = 1/294 (0%) Query: 34 GMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSIL 93 G+ LV+LCI FS F N I QQ ++ + A GMT+VIL G IDLSVGSI+ Sbjct: 20 GIFLSLVMLCIVFSFFNPRFMTVVNFMNILQQVAVVAIAAFGMTWVILLGEIDLSVGSII 79 Query: 94 SISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGL 153 +++ +V ++ L G L G++NG L A + LP FIVT+ T+ RG+ Sbjct: 80 AVAGMVGAQCFAFGMGFAPAIALTLAAGALMGMLNGVLTAKLLLPSFIVTVATMGIYRGM 139 Query: 154 ARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGG 213 L N + + + IG LG+P ++ + + ++ VL +T G + Y GG Sbjct: 140 VSLPTNGAPAMIENETWTAIGTESFLGLPIIIWVVAVLFVINQIVLSKTSFGRRAYLTGG 199 Query: 214 NAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVIL 273 N EAA SGIKV + + ++ +SG++A + GV+ S+RL++A G SYELDAIAA +L Sbjct: 200 NREAAVYSGIKVDRLKILIFMISGVMAAISGVLLSSRLFSAQ-TNAGMSYELDAIAAAVL 258 Query: 274 GGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALD 327 GGTS GG G++VGTL+GALII V++NG+ +L V +Q I+KGLVI+ AV LD Sbjct: 259 GGTSLAGGVGTMVGTLIGALIIGVMNNGMNMLSVPYFYQLIVKGLVILVAVWLD 312 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: 370 Number of extensions: 27 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: 320 Length adjustment: 28 Effective length of query: 309 Effective length of database: 292 Effective search space: 90228 Effective search space used: 90228 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