Align Inner-membrane translocator (characterized, see rationale)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 184 bits (467), Expect = 3e-51 Identities = 116/322 (36%), Positives = 182/322 (56%), Gaps = 8/322 (2%) Query: 64 WPLLALSILLLANLFIDSSFF-NISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGG 122 W + + I+LL L + S+F N + D+ L++I + A+L+ GM+ VI T G Sbjct: 22 WDRVGILIVLLVLLILMSTFAPNFNRVDN-----LLNIARSISVNAILAAGMTFVILTSG 76 Query: 123 IDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIVAT 182 IDLSVG+++A++G V + + I I AG+ VG L G +NG L ++L + P + T Sbjct: 77 IDLSVGSIVAVSGVVSV-VAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVT 135 Query: 183 LLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLLRKTA 242 L M RG+A I +GQ I F +G G +G+P+PV I++ + + +L +T Sbjct: 136 LGTMTFLRGMAYTITEGQPIVSSSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFILERTR 195 Query: 243 LGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGLWL 302 G I AVG NA+A+R G+ K + Y IAG+CA LAG+I A + + AG Sbjct: 196 FGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQP-TAGTGY 254 Query: 303 ELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIVILTV 362 ELDA+ AVV+GG +L GGR +I +++G++I+ L+T +I+ +P LLIK IVI+ Sbjct: 255 ELDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIVIILA 314 Query: 363 LLLQSAKFRRQLSALFKSKRHA 384 + + K +L ++ K A Sbjct: 315 VAIDGLKQHPELFTFWRKKEIA 336 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: 314 Number of extensions: 15 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: 405 Length of database: 339 Length adjustment: 30 Effective length of query: 375 Effective length of database: 309 Effective search space: 115875 Effective search space used: 115875 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 Apr 09 2024. 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