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 AO356_07705 AO356_07705 ABC transporter permease
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07705 Length = 315 Score = 168 bits (425), Expect = 2e-46 Identities = 101/329 (30%), Positives = 178/329 (54%), Gaps = 21/329 (6%) Query: 7 FKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTLM 66 ++++L R + LL + I F+L R+IPG+P +L +++ PEA+ + Sbjct: 6 YRFILSRPLQLLPVLFGISMITFVLVRSIPGDPARALLG-----SRSTPEALIR----IR 56 Query: 67 EEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWI 126 ++GL +P ++QYF F+ L+GDLG S+ Y + LI I TL L+L + ++A + Sbjct: 57 AQYGLDQPLWMQYFYFLKNLLKGDLGQSL-LYKVDALQLISTRIEPTLFLVLGSVLLALL 115 Query: 127 LGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQG 186 + L +AA ++ W D + + +P +WLG++ I L V+LG PV G G Sbjct: 116 IAVPLATVAARNKSGWQDHLIRLFTTAGLGMPAFWLGIMLILLLSVQLGLFPVSGYGRTG 175 Query: 187 TIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKDK 246 W D L H ++P +I ++ +R ++ EL +D+A + G+ ++ Sbjct: 176 ------W----DKLHHMVLPCLTIALALSAVLVRNLRASMLMELQADHATAARARGLSER 225 Query: 247 RIFK-YVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQG 305 IF+ +V NSL+P + LA+++G ++ G ++ E +F PG G LL R + T DY ++QG Sbjct: 226 AIFRRHVLPNSLVPAVNLLAVNIGWLISGTVVIESLFAIPGIGQLLVRGIFTRDYMVVQG 285 Query: 306 IFVILIASIYLANFIVDFLYALIDPRIRL 334 + ++L + NF+ D L +IDPR+ + Sbjct: 286 VAMVLALATVTVNFLADVLTVMIDPRVNM 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: 293 Number of extensions: 19 Number of successful extensions: 5 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 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