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 RR42_RS27425 RR42_RS27425 ABC transporter permease
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__Cup4G11:RR42_RS27425 Length = 324 Score = 176 bits (447), Expect = 6e-49 Identities = 108/327 (33%), Positives = 181/327 (55%), Gaps = 12/327 (3%) Query: 10 LLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTLMEEF 69 +L R + ++ +V T+ F+L RA PG+P+S +++G ++P+ + L +F Sbjct: 7 MLGRVVQGVIAILVIATVNFLLIRAAPGDPVS-VMAG--EAGASDPQFVAQ----LRTQF 59 Query: 70 GLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWILGN 129 GL KP Q ++ + DLG S + V+DLI+ +P TLIL A +++ + G Sbjct: 60 GLDKPVPEQLATYLGHVVHLDLGYSYR-QQQPVLDLILQRLPATLILTGSAFLLSVLFGV 118 Query: 130 SLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQGT-I 188 LGA A+ + +W+D + +L+ P YWL M+ + LF VKL WLP G ++ G + Sbjct: 119 VLGAWASRRAGSWVDNAITLFALVFYATPLYWLAMMAVLLFSVKLDWLPGFGYFTVGADL 178 Query: 189 PNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKDKRI 248 L+ F D+ H ++P ++ + M +A R ++ D+ + G++ RI Sbjct: 179 HGLALVF--DIATHLVLPALTLALFYMAVYARMTRASMLEVAQMDFVKTARAKGVRPGRI 236 Query: 249 FK-YVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQGIF 307 + ++ RN+LLP +T + GG++GGA++TE VF +PG G L+F AL DY L+ G F Sbjct: 237 QRAHILRNALLPVVTLAGIQAGGMIGGAVLTETVFAWPGIGRLMFDALLQRDYNLLLGCF 296 Query: 308 VILIASIYLANFIVDFLYALIDPRIRL 334 ++ A L N + DF+Y L+DPRI + Sbjct: 297 LVTAAMAVLFNLLTDFVYTLVDPRIEM 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: 284 Number of extensions: 14 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