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 3609627 Dshi_3010 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__Dino:3609627 Length = 339 Score = 232 bits (591), Expect = 1e-65 Identities = 123/333 (36%), Positives = 199/333 (59%), Gaps = 6/333 (1%) Query: 9 YLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRV--AQANPEAIRAAERTLM 66 YL+ R I ++T +A T+++++PR P +P +LS ++ A A+ EAI A R Sbjct: 8 YLINRTITFVLTVFIAATLIWLIPRFSPVDPAEIMLSRMAAGGGAVADSEAILAQLRA-- 65 Query: 67 EEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWI 126 +FGL P VQY +++ L +LG S +P V LI +PWTL L++ + ++ ++ Sbjct: 66 -DFGLNDPLIVQYLKYMGNLLTFNLGISTASFPTPVSVLIAQALPWTLGLMILSVVITFV 124 Query: 127 LGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQG 186 +GN+LGA ++R I K V+ T +I + IP G++ +++F + L WLP+ G+Y Sbjct: 125 IGNALGAFMVWERTPKIWKVVIPTFMIFTSIPPILSGLLLMYIFSITLRWLPLTGSYGLT 184 Query: 187 TIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKDK 246 P W+F V++H +P SI+V G W +GMR ++I G DY ++ G+K + Sbjct: 185 VEPGWDWAFISSVIEHGTLPALSIIVVTFGFWTLGMRGLMISVQGEDYVNLAKAKGLKPR 244 Query: 247 RI-FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQG 305 + +KY+ RN++LPQIT AL +G ++ G ++ E +F Y G G LL+ A+ D+ +IQG Sbjct: 245 YVLYKYMVRNAILPQITAFALKIGLLVSGQILVERIFGYNGMGKLLYDAILDQDFAVIQG 304 Query: 306 IFVILIASIYLANFIVDFLYALIDPRIRLGQEA 338 + I+I L+ F+VD +Y LIDPRIRL +EA Sbjct: 305 VSYIIILMTALSVFLVDLIYPLIDPRIRLSEEA 337 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: 371 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: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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