Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 270 bits (690), Expect = 4e-77 Identities = 146/299 (48%), Positives = 205/299 (68%), Gaps = 1/299 (0%) Query: 33 LGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSI 92 +G+L VL++L I S NF NL IA+ S+N +LAAGMTFVILT GIDLSVGSI Sbjct: 25 VGILIVLLVLLILMSTFAPNFNRVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSI 84 Query: 93 LSISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRG 152 +++S VV+++ ++ L++ A + G L G++NG L A++ L PFIVTLGT+T +RG Sbjct: 85 VAVSGVVSVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVTLGTMTFLRG 144 Query: 153 LARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVG 212 +A + I + + F +GNG ++G+P VII V ++WF+L RT G IYAVG Sbjct: 145 MAYTITEGQPIVSSSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFILERTRFGRHIYAVG 204 Query: 213 GNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVI 272 GNA+AARL+G++V VL VY ++G+ AGL G++ +AR+ +A G YELDAIAAV+ Sbjct: 205 GNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQP-TAGTGYELDAIAAVV 263 Query: 273 LGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRR 331 LGGTS GG G I+GTL+G++I+ VLS GL+LL V Q +IKG+VII AVA+D ++ Sbjct: 264 LGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIVIILAVAIDGLKQ 322 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: 368 Number of extensions: 20 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: 339 Length adjustment: 28 Effective length of query: 309 Effective length of database: 311 Effective search space: 96099 Effective search space used: 96099 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