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 WP_086508116.1 BZY95_RS00860 ABC transporter permease
Query= TCDB::Q9WXN7 (338 letters) >NCBI__GCF_002151265.1:WP_086508116.1 Length = 326 Score = 187 bits (475), Expect = 3e-52 Identities = 111/331 (33%), Positives = 183/331 (55%), Gaps = 21/331 (6%) Query: 9 YLLRRFIF-LLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTLME 67 YL+RR + L+ +I+AT + F+ +P + I GLS + E IRA+ Sbjct: 7 YLIRRVLHGLMALFIIATLLFFLFRLGLPDPTAALITEGLSPEER---ERIRAS------ 57 Query: 68 EFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWIL 127 FGL +P + QYF ++ L+GD G S Y V D+I + T++L+LPA ++A+ + Sbjct: 58 -FGLDRPIWEQYFLYLANILQGDFGYSF-HYRAPVADIIWERLGNTMVLMLPAILLAYAV 115 Query: 128 GNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQGT 187 G LGA +++R + D + L+ P +W GMI I +FG+ LGWLP G T Sbjct: 116 GVPLGAWLSWRRGSRTDTTGIFVGLMFRSAPMFWTGMIAILVFGIALGWLPTSG---MRT 172 Query: 188 IPNLSWSFF-----VDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLG 242 +P + FF +D L H I+P + + +G + MR ++ G D+ + G Sbjct: 173 LPYEATGFFDKIFTLDFLHHLILPALVVALYYLGSPLLIMRNTMLEVYGEDFIEMARAKG 232 Query: 243 MKDKRI-FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYP 301 + ++RI + + RN+LLP +T LA+++G GG ++ E+VF++PG G + ++ T D+P Sbjct: 233 LPERRILYAHAARNALLPVVTQLAVTVGLAAGGQVVVEVVFSWPGLGREILNSVRTSDFP 292 Query: 302 LIQGIFVILIASIYLANFIVDFLYALIDPRI 332 L Q F+++ A + N +VD LY L+DPR+ Sbjct: 293 LAQASFLVMAAFVVTLNLLVDILYTLLDPRV 323 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: 330 Number of extensions: 24 Number of successful extensions: 6 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 24 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