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_085637999.1 MGEO_RS12315 ABC transporter permease
Query= TCDB::Q9WXN7 (338 letters) >NCBI__GCF_002115805.1:WP_085637999.1 Length = 326 Score = 153 bits (387), Expect = 5e-42 Identities = 97/331 (29%), Positives = 177/331 (53%), Gaps = 13/331 (3%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 M Y++RR + ++ + F + R + G+P+ +L G R A+ ER L Sbjct: 1 MLAYIIRRVGQSALVLLIVGLVAFAMFRFV-GDPIDNML-GQERTAED-------IER-L 50 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 + GL +P+ VQY++F+ A++G+ G S R V ++++ P TL L + + ++A Sbjct: 51 RSQLGLDQPFVVQYYKFLEGAVQGNFGVSYR-QGRPVAEILLERAPATLELAMVSGVLAI 109 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185 + G +LG A +R+ + +++ SLI +P + +G++ I+LF V+LGWLP G Sbjct: 110 LFGIALGVFTAIRRDGVLANAIMSASLIGVSLPTFLIGILLIYLFSVELGWLPSFGRGET 169 Query: 186 GTIPNLSWSFFVDV-LKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMK 244 + + F + LK I+P ++ + M +R ++ L DY F+ G++ Sbjct: 170 VDLGGWTTGFLTESGLKALILPSITLGLYQMTLIMRLVRSEMLEVLRQDYIRFARARGLR 229 Query: 245 DKRI-FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLI 303 D+ + F++ +N+++P IT + L LG ++ A+ITE VF +PG G L A+ +D P++ Sbjct: 230 DRAVNFRHALKNTMVPVITVIGLQLGAIIAFAIITETVFQWPGVGLLFINAVQFVDIPVM 289 Query: 304 QGIFVILIASIYLANFIVDFLYALIDPRIRL 334 +++ N +VD LY IDPR+R+ Sbjct: 290 AAYLMLISVMFVGINLLVDILYFFIDPRLRV 320 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: 281 Number of extensions: 21 Number of successful extensions: 3 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