Align Inner-membrane translocator (characterized, see rationale)
to candidate RR42_RS03365 RR42_RS03365 ribose ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__Cup4G11:RR42_RS03365 Length = 333 Score = 187 bits (474), Expect = 5e-52 Identities = 108/268 (40%), Positives = 169/268 (63%), Gaps = 3/268 (1%) Query: 109 LLSIGMSLVIATGGIDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCING 168 +L+ GM+ VI TGGIDLSVG++++I+ V + L+P + +++V AA L+ GLL G +NG Sbjct: 67 VLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGMLSVPAA-LLCGLLFGIVNG 125 Query: 169 GLVSFLGIQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVI 228 LV+F+ + P + TL + A RG+A+L+ I GFA IG G+ LG+P V I Sbjct: 126 ALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAF 185 Query: 229 GMLTFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTA 288 ++ S +LR+T LGL I AVG NA+A+R GI + LF Y ++GL A L G++S+A Sbjct: 186 AVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSA 245 Query: 289 DIQGSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPA 348 + ++ G ELDA+ AV++GG + GG S++ ++VGALII L+ +++ G+ Sbjct: 246 RLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSD 305 Query: 349 KFNLLIKAIVILTVLLLQSAKFRRQLSA 376 + +IK +VI+ + L S +RR+ SA Sbjct: 306 IWQYIIKGLVIIGAVALDS--YRRKGSA 331 Lambda K H 0.323 0.136 0.379 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: 315 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 405 Length of database: 333 Length adjustment: 30 Effective length of query: 375 Effective length of database: 303 Effective search space: 113625 Effective search space used: 113625 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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