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_085636090.1 MGEO_RS07445 ABC transporter permease
Query= TCDB::Q9WXN7 (338 letters) >NCBI__GCF_002115805.1:WP_085636090.1 Length = 315 Score = 145 bits (366), Expect = 1e-39 Identities = 101/329 (30%), Positives = 168/329 (51%), Gaps = 16/329 (4%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 M Y+L+R + + + + IVF++ IPG+P + IL + A PE + R L Sbjct: 1 MAGYILKRLVSAIPVLLGISVIVFVIMAMIPGDPATAILG-----SYATPENVEKLNRDL 55 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 GL KP +YF ++ L+GD G S + R V+D ++ TLIL + ++ Sbjct: 56 ----GLDKPMVQRYFIWLGNMLQGDFGRSFSLN-RAVLDEVMERFGATLILAGTSFVLCS 110 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185 ILG + G ++A ++ + DK + L+ IP ++LGM+ I +F V+L W PV G + Sbjct: 111 ILGIAAGVVSAARQYGFADKAITFAVLLGISIPSFFLGMMMILIFAVQLRWFPVSGMWPI 170 Query: 186 GTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKD 245 +LS ++ H +P ++ V A G A R ++ L D+ + G+ + Sbjct: 171 YGARDLS-----ALISHLTLPALALAVVATGVIARLSRSAMLEVLRQDFIRTARAKGVHE 225 Query: 246 KR-IFKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQ 304 + I+++ R +++ I L + G VL GA+ E+VF +PG G +L A+ D L+Q Sbjct: 226 RSVIWRHALRAAMVSIIPVLGVQAGFVLSGAVYIEMVFQWPGVGRMLVDAILKRDILLVQ 285 Query: 305 GIFVILIASIYLANFIVDFLYALIDPRIR 333 G V + A L N VD +L+DPRI+ Sbjct: 286 GGVVFVAACYVLFNIAVDVAQSLLDPRIK 314 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: 272 Number of extensions: 16 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: 315 Length adjustment: 28 Effective length of query: 310 Effective length of database: 287 Effective search space: 88970 Effective search space used: 88970 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: 48 (23.1 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