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 AZOBR_RS23020 AZOBR_RS23020 ABC transporter permease
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__azobra:AZOBR_RS23020 Length = 326 Score = 174 bits (440), Expect = 4e-48 Identities = 101/327 (30%), Positives = 168/327 (51%), Gaps = 10/327 (3%) Query: 9 YLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTLMEE 68 ++ +R + + + F L A PG+P + +++G + A A L ++ Sbjct: 7 FISQRLVKAVFVILAIAVFNFFLVHAAPGDPAA-VMAGEAGAADAK------FVEQLRQQ 59 Query: 69 FGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWILG 128 FGL +P Y Q +++K ++ DLG S R V DL++ +P TL L L A ++A + G Sbjct: 60 FGLDRPLYEQLGTYMSKVVQADLGYSYR-QQRPVFDLLMDRLPVTLSLTLTAFVLALLGG 118 Query: 129 NSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQGTI 188 +LG LAA + TW D + L P +W+G++ I LF V LGWLP G S G Sbjct: 119 VALGTLAAMRAGTWSDTAITVVGLTAYATPIFWIGLMLILLFSVNLGWLPAFGTESIGA- 177 Query: 189 PNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKDKRI 248 W F+D KH ++P ++ + M + R ++ D+ + G+ + RI Sbjct: 178 GYTGWDAFLDRAKHLVLPVTTLGLFYMAVYTRLTRASILEVRDMDFVKTARAKGLPEWRI 237 Query: 249 FK-YVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQGIF 307 ++ RN++LP IT G ++GG+++ E VF PG G L F A+ DY ++ GIF Sbjct: 238 VSVHILRNAILPVITVAGFQAGHLIGGSILIETVFALPGIGRLAFEAVLQRDYQVLLGIF 297 Query: 308 VILIASIYLANFIVDFLYALIDPRIRL 334 ++ + + N + D +Y+L+DPRI + Sbjct: 298 LLTSVVVVVFNLLTDLIYSLVDPRIEV 324 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: 283 Number of extensions: 15 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: 326 Length adjustment: 28 Effective length of query: 310 Effective length of database: 298 Effective search space: 92380 Effective search space used: 92380 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: 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