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 BWI76_RS19200 BWI76_RS19200 binding-protein-dependent transport system inner membrane protein
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__Koxy:BWI76_RS19200 Length = 312 Score = 169 bits (427), Expect = 1e-46 Identities = 106/329 (32%), Positives = 178/329 (54%), Gaps = 21/329 (6%) Query: 7 FKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTLM 66 +++LL R + LL + + I F++ RAIPG+P ++IL G+ + AA + Sbjct: 4 YRFLLLRPLQLLPVLLGISLITFMMVRAIPGDP-ARILLGV--------RSTPAALARIR 54 Query: 67 EEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAWI 126 +FGL +P +VQY F+ L+G+LG SI Y + LI + TL L+L + ++A Sbjct: 55 AQFGLDEPLWVQYGYFLRNLLQGELGKSIV-YRVDTLKLIASRLEPTLWLVLGSVLLAIA 113 Query: 127 LGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQG 186 L L A+AA +R D+ + + P +WLG++ I LF + LGW PV G S Sbjct: 114 LTVPLAAMAARQRGRLADRLIRLFTTAGLGFPAFWLGIMLILLFSIVLGWFPVSGYGSD- 172 Query: 187 TIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKDK 246 FVD L H ++P ++ ++ +R ++ E+ SDY + + G +++ Sbjct: 173 ---------FVDQLHHMVLPCLTVALALSAVLIRNLRASLLMEMNSDYVVAARARGQQER 223 Query: 247 RIF-KYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQG 305 RIF ++V NSL+P I LA+++G +G ++ E VF PG G LL +A+ + DY ++QG Sbjct: 224 RIFWRHVLPNSLVPTINLLAVNIGWFIGSTVVIESVFAIPGLGQLLVKAIFSRDYMVVQG 283 Query: 306 IFVILIASIYLANFIVDFLYALIDPRIRL 334 + ++ + + + D L +DPRI+L Sbjct: 284 VVMVFALATVAVSLLADILTVALDPRIKL 312 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: 294 Number of extensions: 13 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: 312 Length adjustment: 28 Effective length of query: 310 Effective length of database: 284 Effective search space: 88040 Effective search space used: 88040 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