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 15607 b1486 D-ala-D-ala transporter subunit (NCBI)
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__Keio:15607 Length = 340 Score = 157 bits (397), Expect = 4e-43 Identities = 112/345 (32%), Positives = 176/345 (51%), Gaps = 26/345 (7%) Query: 7 FKYLLRRFIFLLVTYIVATTIV-FILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 F +LR+ + LV + ++ FI+ IPG+P +++L+G R + A E IR Sbjct: 3 FWSILRQRCWGLVLVVAGVCVITFIISHLIPGDP-ARLLAG-DRASDAIVENIR------ 54 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 ++ GL +P YVQ++ +++ GDLGTSI R V++ + P TL L A ++A Sbjct: 55 -QQLGLDQPLYVQFYRYVSDLFHGDLGTSIRT-GRPVLEELRIFFPATLELAFGALLLAL 112 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLP------- 178 ++G LG L+A RN W+D V ++ P +WLG+ I LF L LP Sbjct: 113 LIGIPLGILSAVWRNRWLDHLVRIMAITGISTPAFWLGLGVIVLFYGHLQILPGGGRLDD 172 Query: 179 -------VQGAYSQGTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELG 231 V G Y + + F + L+H I+P ++ +G A +R ++ +L Sbjct: 173 WLDPPTHVTGFYLLDALLEGNGEVFFNALQHLILPALTLAFVHLGIVARQIRSAMLEQLS 232 Query: 232 SDYAMFSEYLGMKDKRIFK-YVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYL 290 DY + G+ I Y N+L+P IT L L+LG +L GA++TE VF +PG G Sbjct: 233 EDYIRTARASGLPGWYIVLCYALPNALIPSITVLGLALGDLLYGAVLTETVFAWPGMGAW 292 Query: 291 LFRALTTLDYPLIQGIFVILIASIYLANFIVDFLYALIDPRIRLG 335 + ++ LD+P + G V++ + L N +VD LY IDPRI G Sbjct: 293 VVTSIQALDFPAVMGFAVVVSFAYVLVNLVVDLLYLWIDPRIGRG 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: 337 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 338 Length of database: 340 Length adjustment: 28 Effective length of query: 310 Effective length of database: 312 Effective search space: 96720 Effective search space used: 96720 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