Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__HerbieS:HSERO_RS05325 Length = 328 Score = 270 bits (691), Expect = 3e-77 Identities = 138/318 (43%), Positives = 208/318 (65%), Gaps = 2/318 (0%) Query: 2 NAKTITAPVTAAPRNRLRLSLDRFGLPLV-FILLCVVMAFSSEYFMTWRNWMDILRQTSI 60 NA + TAA L LPL +++ ++M +S+ F T NW ++LRQ SI Sbjct: 6 NALPAASLHTAASARWRSLIHSPLALPLAGLVVVSLLMGLASDNFFTLSNWFNVLRQVSI 65 Query: 61 NGILAVGMTYVILTKGIDLSVGSILAFAGLCSA-MVATQGYGLLAAVSAGMFAGAMLGVV 119 GILAVGM++VILT GIDLSVG+ +A AG SA ++ G A+ G+ +G++ Sbjct: 66 VGILAVGMSFVILTGGIDLSVGAAMALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLL 125 Query: 120 NGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIII 179 NG +VA +P + TL + +ARG+ I + G PI+ LP G+G+IG + VP+I+ Sbjct: 126 NGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWISWFGVGRIGMVPVPVIL 185 Query: 180 FAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVL 239 +V + W++L+ T +GR+VYA+GGNE +AR SG+ ++ +VY +SG +GLA ++L Sbjct: 186 MLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGLAAIIL 245 Query: 240 SARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVS 299 + R S P AGV +ELDAIAAVV+GGT+++GG G +VGTL GA+L+G++NNGLNL+G++ Sbjct: 246 TGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLNLMGIN 305 Query: 300 SYYQQVAKGLIIVFAVLI 317 Y Q + +G+II+ A+ I Sbjct: 306 PYLQDIIRGVIILLAIYI 323 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: 283 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: 325 Length of database: 328 Length adjustment: 28 Effective length of query: 297 Effective length of database: 300 Effective search space: 89100 Effective search space used: 89100 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