Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate WP_083529298.1 AS188_RS06770 ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >NCBI__GCF_001482365.1:WP_083529298.1 Length = 366 Score = 134 bits (337), Expect = 4e-36 Identities = 110/343 (32%), Positives = 173/343 (50%), Gaps = 23/343 (6%) Query: 8 PAASTGAPLPAGTLGRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQAS 67 P A+ A T G L +G L V++ + F++ + Q++S + AS Sbjct: 24 PTAAAPADERVQTRGLLGALLARPEIGALVGAVVVGLFFAIAAPSITQAQSISTVLYGAS 83 Query: 68 INMVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGM-LSVPAALLCGLLFGI 126 ++ G++ +++ G DLS G + SA+ A L S L + + V ALL L G+ Sbjct: 84 TIGIMVVGVSLLMIGGEFDLSTGVAVISSALTASLFSWYFGLNVWVGVAVALLTSLAIGL 143 Query: 127 VNGALVAFMKLPPFIVTLGTLTAVRGL----ARLVGNDSTIYNPDI----GFA-----FI 173 VNG L+ KLP FIVTL T + GL RL+G ++ +P I GFA F Sbjct: 144 VNGVLLMRTKLPSFIVTLATFLMLTGLNLALTRLIGG--SVSSPSISGMDGFAAAKAVFA 201 Query: 174 GNGEVLGVPWLVIIAF--AVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLF 231 + EV GV + + + A+VA++ FVL +T +G I+AVGG+ +AAR G+ V + Sbjct: 202 SSVEVGGVSIRITVFYWIALVAIASFVLLKTRIGNWIFAVGGDPDAARAVGVPVARTKIG 261 Query: 232 VYAVSGLLAGLGGVMSSARLYAANGLQLGQSY--ELDAIAAVILGGTSFVGGTGSIVGTL 289 ++ GL A L G+ + L+A + +Q G+ E I ++GG GG GS +G Sbjct: 262 LFMGVGLCAWLVGMHN---LFAFDSVQSGEGVGNEFLYIIGAVIGGCLLTGGFGSAIGGA 318 Query: 290 VGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRK 332 +GALI + S G+V + W GL+++ A ++ Y RK Sbjct: 319 IGALIFGIASRGIVYAEWNPDWFKFFLGLMLLLATIVNMYVRK 361 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: 393 Number of extensions: 22 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: 366 Length adjustment: 29 Effective length of query: 308 Effective length of database: 337 Effective search space: 103796 Effective search space used: 103796 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 24 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