Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Koxy:BWI76_RS00280 Length = 321 Score = 226 bits (575), Expect = 8e-64 Identities = 136/302 (45%), Positives = 188/302 (62%), Gaps = 8/302 (2%) Query: 35 MLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILS 94 ++ +LVL+ I S ++ NF NL I QQ S+N ++A GMT VILT GIDLSVGS+L+ Sbjct: 23 LIALLVLIAI-VSTMSPNFFTVNNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLA 81 Query: 95 ISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLA 154 ++ VA + + +++V AAL G G V G +VA ++ FI TL + +RG+ Sbjct: 82 LTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVT 141 Query: 155 RLVGNDSTIY-----NPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIY 209 + N S + N D+ F + G G LG+P V I V +W++L T LG IY Sbjct: 142 MVYTNGSPVNTGFTDNADL-FGWFGIGRPLGIPTPVWIMAIVFLAAWYMLHHTRLGRYIY 200 Query: 210 AVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIA 269 A+GGN A RLSGI V V + VY++ G+LA L G++ ARL +A G YELDAIA Sbjct: 201 ALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSSAQPTA-GTGYELDAIA 259 Query: 270 AVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSY 329 AV+LGGTS GG G IVGTL+GALI+ L+NGL LLGVS +Q I+K +VI+ AV +D+ Sbjct: 260 AVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVDNK 319 Query: 330 RR 331 ++ Sbjct: 320 KQ 321 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: 341 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 337 Length of database: 321 Length adjustment: 28 Effective length of query: 309 Effective length of database: 293 Effective search space: 90537 Effective search space used: 90537 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 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