Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate Ac3H11_606 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_606 Length = 337 Score = 164 bits (414), Expect = 4e-45 Identities = 111/315 (35%), Positives = 174/315 (55%), Gaps = 15/315 (4%) Query: 29 RLRALGMLPVLVLLCIGFSVLTENFAG--WQN------LSIIAQQASINMVLAAGMTFVI 80 R R L L LL + +V +F W++ L I +A+ ++++ GMT VI Sbjct: 3 RHRLAWPLITLALLLVVNTVFNSSFLHIEWRDGHLYGSLIDILNRAAPLVLVSLGMTLVI 62 Query: 81 LTGGIDLSVGSILSISAVVAMLV---SLMPQLGMLSVPAALL----CGLLFGIVNGALVA 133 T GID+SVG+ ++I+A VA + S+ +P A+L LL G+ NG LVA Sbjct: 63 ATRGIDISVGATVAIAAAVAAWMIGGSVSGTESRFPLPVAILGAIGVALLCGLWNGVLVA 122 Query: 134 FMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVA 193 + + P I TL + A RG+A+L+ + I + F+G G + G+P+ V + AV Sbjct: 123 KVGMQPIIATLILMVAGRGIAQLITDGQIITIYYTPYFFLGGGYLAGLPFSVFVVAAVFV 182 Query: 194 VSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYA 253 + + RT LGL I AVG N AAR++G++ +++ Y G+ AG+ G++ S+ + + Sbjct: 183 ALYLAITRTALGLFIQAVGINPTAARVAGVQAGRLIVAAYVFCGVCAGIAGLLISSNVKS 242 Query: 254 ANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQY 313 A+G GQ ELDAI AV LGGT+ GG S+VG+++GALII L+ + LGV Sbjct: 243 ADGNNAGQLLELDAILAVTLGGTALTGGRFSLVGSVIGALIIQTLTYAIYSLGVPPEINL 302 Query: 314 IIKGLVIIGAVALDS 328 ++K +V+ + L S Sbjct: 303 VVKAVVVFIVMLLQS 317 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: 344 Number of extensions: 18 Number of successful extensions: 2 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: 337 Length adjustment: 28 Effective length of query: 309 Effective length of database: 309 Effective search space: 95481 Effective search space used: 95481 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 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