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 HSERO_RS07870 HSERO_RS07870 ABC transporter permease
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__HerbieS:HSERO_RS07870 Length = 324 Score = 156 bits (395), Expect = 6e-43 Identities = 98/327 (29%), Positives = 163/327 (49%), Gaps = 13/327 (3%) Query: 10 LLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTLMEEF 69 + R + L+ ++ T IVF I GNP+ ++ + + +++E Sbjct: 5 IARSVVQALMVVLLMTVIVFFGLHMI-GNPVDILIG---------QDVDQVDRLRIIQEL 54 Query: 70 GLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWILGN 129 GL +P + QY F+ AL G+LG S Y I LI +P TL L A ++A ++G Sbjct: 55 GLDQPVWRQYLAFLNGALHGNLGNSFV-YNTPAILLIFQRLPATLELACAALLLALVVGV 113 Query: 130 SLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQGTIP 189 LG A K + + V+TTS+ +P +W+G++ I F V LGWLP G + Sbjct: 114 PLGLFAGMKPDHPFSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELF 173 Query: 190 NLSWSFFV-DVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKDKRI 248 + WS+ D +H I+P ++ + + R V L D+ F+ G+ R+ Sbjct: 174 GVQWSWLTADGWRHMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARV 233 Query: 249 -FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQGIF 307 YV RN+L+P +T + L G + A++TE +F +PG G L+ ++ LD P+I Sbjct: 234 VLMYVLRNTLIPLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYL 293 Query: 308 VILIASIYLANFIVDFLYALIDPRIRL 334 ++++ N +VD LY L+DPR+R+ Sbjct: 294 MVIVCMFVTINLVVDVLYKLLDPRVRV 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: 280 Number of extensions: 17 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: 324 Length adjustment: 28 Effective length of query: 310 Effective length of database: 296 Effective search space: 91760 Effective search space used: 91760 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