Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__BFirm:BPHYT_RS20745 Length = 341 Score = 232 bits (592), Expect = 9e-66 Identities = 123/302 (40%), Positives = 192/302 (63%), Gaps = 9/302 (2%) Query: 32 ILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAF-AGL 90 ILL V +F+S FM N + IL+ T++NG+LA+ T+VI+T GIDLSVG+++ F A + Sbjct: 39 ILLLVFFSFASPAFMQMDNMLGILQATAVNGVLAIACTFVIITGGIDLSVGTLMTFTAVI 98 Query: 91 CSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTFILN 150 C + + V A + GA+ G V+G + A + IPPF+ATLGM+ + +G++ +++ Sbjct: 99 CGVFLTYWHLPMWTGVLAAIGTGAICGTVSGTLTAKMKIPPFIATLGMMMLLKGLSLVVS 158 Query: 151 DGSPI--TDLPDAYLALGIGKIG------PIGVPIIIFAVVALIFWMVLRYTTYGRYVYA 202 PI TD + Y+ IG P+ ++I +A++ + L T GRY +A Sbjct: 159 ADKPIYFTDTENFYMISQDSLIGDLLPSLPVPNAVLILFFLAVVSSITLNRTALGRYTFA 218 Query: 203 VGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAV 262 +G NE++ R SG+ V + ++Y +SG + G+AG+++++R SA P G YEL+AIAAV Sbjct: 219 LGSNEEAVRLSGVNVDRWKIAIYGLSGAICGIAGLLIASRLNSAQPALGQGYELEAIAAV 278 Query: 263 VIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRK 322 VIGGTSLSGG G+I+GT+ GA ++ V+ NGL ++ V+ +Q V GLII+ AV D+ R+ Sbjct: 279 VIGGTSLSGGAGTILGTIIGAFIMSVLTNGLRIMSVAQEWQIVVTGLIIILAVYGDILRR 338 Query: 323 KK 324 KK Sbjct: 339 KK 340 Lambda K H 0.326 0.141 0.412 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: 246 Number of extensions: 13 Number of successful extensions: 4 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: 325 Length of database: 341 Length adjustment: 28 Effective length of query: 297 Effective length of database: 313 Effective search space: 92961 Effective search space used: 92961 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 (21.6 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