Align TM0029, 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_RS27420 RR42_RS27420 ABC transporter permease
Query= TCDB::Q9WXN6 (280 letters) >FitnessBrowser__Cup4G11:RR42_RS27420 Length = 280 Score = 147 bits (372), Expect = 2e-40 Identities = 85/283 (30%), Positives = 144/283 (50%), Gaps = 14/283 (4%) Query: 1 MFRTMIRPLFKNKKFIIGFSIFLFFLFLGIFGPMFYRVDPTEMTWDYEQPP------SSA 54 M T R +NK ++G + F L +FGP DP WD Q P Sbjct: 1 MKNTFWRRFCRNKAAVLGMVVLAGFAVLALFGPWMAGHDP----WDMVQQPFLQPMQEPG 56 Query: 55 HPLGTDTYGRDVLAQLLHGIRSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVLMGIT 114 +GTDT GRD+LA ++HG R SL IG ++ ++SL+IG +G+ S G +D LM T Sbjct: 57 FAMGTDTMGRDILAGVIHGARISLLIGVVSTVVSLLIGVTLGAISGYFGGWIDAALMRFT 116 Query: 115 NIVLTTPSILIAILIASYLKVRSVEMVAVILGLFQWPWFARAIRAQLMSVMSREYVYLSV 174 + PS +A+++ + + S+ + + + WP AR +R++ +++ R++V + Sbjct: 117 ELFQAVPSFALALVLVAIFE-PSIGSIVAAIAIVSWPPVARLVRSEFLTLRQRDFVQAAK 175 Query: 175 MAGYSDLRLVIEDLIPTIATYAFMSFVLFINGGIMGEAGLSLIGLGPTQGISLGIMLQWA 234 +AG S R+++ ++P ++ + L + I+ E+ LS +GLG +S G M+ A Sbjct: 176 LAGQSTPRIILSQILPNASSPIVVMASLMVATAILLESSLSFLGLGDPNHMSWGYMVGSA 235 Query: 235 VLMEAVRRGLWWWFVPPGLAIVAVTASLLVISTAMDEVFNPRL 277 V R WW V PG AI+ +L ++ +++ N RL Sbjct: 236 ---RTVLRQAWWMAVFPGTAILLTVLALNMVGEGLNDALNARL 275 Lambda K H 0.330 0.144 0.441 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: 197 Number of extensions: 15 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: 280 Length of database: 280 Length adjustment: 26 Effective length of query: 254 Effective length of database: 254 Effective search space: 64516 Effective search space used: 64516 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: 47 (22.7 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