Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate Pf1N1B4_6033 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6033 Length = 325 Score = 184 bits (467), Expect = 3e-51 Identities = 112/301 (37%), Positives = 169/301 (56%), Gaps = 4/301 (1%) Query: 27 LPLVFILLCVVMAFS--SEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSI 84 L L LL +V FS S +F+++ + + Q +LAVGMT+V++ GIDLSVGS+ Sbjct: 21 LGLAGALLAMVALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSV 80 Query: 85 LAFAGLC-SAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIAR 143 LA A S + G+ +L A GM A+ G + G + IP F+ +LG+L +AR Sbjct: 81 LALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGVLEMAR 140 Query: 144 GMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAV 203 G+ + + GS + DA+ L I II ++ I VL T +GRY+ + Sbjct: 141 GLAYQMT-GSRTAYIGDAFAWLSNPIAFGISPSFIIALLIIFIAQAVLTRTVFGRYLIGI 199 Query: 204 GGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVV 263 G NE++ R +GI + V+ + GLLAG+A + +R +A P AG EL IAAVV Sbjct: 200 GTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNAGSGLELQVIAAVV 259 Query: 264 IGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRKK 323 IGGTSL GG GS++ T FG L+I V+ GL +G + +++ G +IV AV++D +R + Sbjct: 260 IGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTYRSQ 319 Query: 324 K 324 + Sbjct: 320 R 320 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: 236 Number of extensions: 9 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: 325 Length of database: 325 Length adjustment: 28 Effective length of query: 297 Effective length of database: 297 Effective search space: 88209 Effective search space used: 88209 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: 48 (23.1 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