Align TM0030, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate RR42_RS07945 RR42_RS07945 ABC transporter permease
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__Cup4G11:RR42_RS07945 Length = 316 Score = 180 bits (456), Expect = 5e-50 Identities = 103/325 (31%), Positives = 177/325 (54%), Gaps = 13/325 (4%) Query: 9 YLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTLMEE 68 YLLRR ++ + + + F L PG+PL +L P+A R L Sbjct: 3 YLLRRIVYAIPILLGVALLCFSLVHIAPGDPLVSVLP---------PDASEDLRRQLTAL 53 Query: 69 FGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWILG 128 +G KP+ Q+ ++T+AL GDLGTSI R V+ ++ + ++ L AT++ + G Sbjct: 54 YGFDKPFVEQFLHWLTRALHGDLGTSIATN-RPVMSEVMTAVINSVRLAAVATLIGFTFG 112 Query: 129 NSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQGTI 188 G +A Y R++ D+ S+ +P+YWLGM+ + +F V LGWLP GA G+ Sbjct: 113 CLFGFVAGYFRDSAADRTASFLSVFGVSMPHYWLGMVLVIVFSVFLGWLPATGAGPGGSS 172 Query: 189 PNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKDKRI 248 W++ + +++ ++P ++ V MG A +R +V L +++ + + G+ + + Sbjct: 173 ---DWAWNWEHIQYMVLPAVTMSVIPMGIVARTIRALVAEILSNEFIVGLKARGLSELAV 229 Query: 249 FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQGIFV 308 F++V +N ++ + L LG +LGG+++ E VF++PGTG+LL A+ D+PL+QG + Sbjct: 230 FRHVLKNVAPTALSVMGLQLGYLLGGSILIETVFSWPGTGFLLNSAIFQRDFPLLQGTIL 289 Query: 309 ILIASIYLANFIVDFLYALIDPRIR 333 +L L N +VD L L DPRI+ Sbjct: 290 VLAVFFVLLNLLVDALQTLFDPRIQ 314 Lambda K H 0.329 0.146 0.449 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: 311 Number of extensions: 18 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: 338 Length of database: 316 Length adjustment: 28 Effective length of query: 310 Effective length of database: 288 Effective search space: 89280 Effective search space used: 89280 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 (21.8 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