Align Inner-membrane translocator (characterized, see rationale)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 160 bits (405), Expect = 4e-44 Identities = 99/270 (36%), Positives = 151/270 (55%), Gaps = 12/270 (4%) Query: 15 LLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSG 74 LL+ + L+ TF F + N+ R + I A GMT VI++ GIDLSVG+++A+SG Sbjct: 31 LLVLLILMSTFA-PNFNRVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSIVAVSG 89 Query: 75 VVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLATT 134 VV+ + PL A + + +G L G L G + L PFIVTL M RG+A T Sbjct: 90 VVSVVAAMAGIPAPL-AILAGVGVGALCGLLNGVLTAYLALAPFIVTLGTMTFLRGMAYT 148 Query: 135 LSEESIAIDHPFYDAVAEMSIALPGNGAL---DLSSLIFILFFVIIAVVMHYTRFGTNVY 191 ++E + + +S GNG L + +I ++ +++ ++ TRFG ++Y Sbjct: 149 ITEGQPIVS-------SSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFILERTRFGRHIY 201 Query: 192 AIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIAA 251 A+GGN +A L G+ + + ++Y I+ A LAGI+F S G ELDAIAA Sbjct: 202 AVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPTAGTGYELDAIAA 261 Query: 252 VVIGGTLLTGGSGFVLGTVLGVILMGVIQT 281 VV+GGT L GG G ++GT++G I++GV+ T Sbjct: 262 VVLGGTSLAGGRGRIIGTLIGSIILGVLST 291 Lambda K H 0.330 0.145 0.424 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: 365 Number of extensions: 21 Number of successful extensions: 5 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: 320 Length of database: 339 Length adjustment: 28 Effective length of query: 292 Effective length of database: 311 Effective search space: 90812 Effective search space used: 90812 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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