Align Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate SMc03814 SMc03814 ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__Smeli:SMc03814 Length = 335 Score = 228 bits (580), Expect = 2e-64 Identities = 125/312 (40%), Positives = 186/312 (59%), Gaps = 6/312 (1%) Query: 1 MWKKLFKAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIIT 60 +W ++F A+E I L ++ I + + V + +F T N+ + N FI IM+ GMT V+I+ Sbjct: 22 LWSRVFLAQETWIALAILVIGLVVSVISAKFATSGNLLNIFQNACFIGIMALGMTPVLIS 81 Query: 61 SGIDLSVGSILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFI 120 GID+SVGSILG V +G++++ + + ++ LA+GV G+ NG++I+ +L PFI Sbjct: 82 GGIDISVGSILGMCGVTLGIVLNSD-MPLAVGILATLAMGVACGMVNGIIISYVKLPPFI 140 Query: 121 STLGMLSVGRGLAYVMSGGWPISPFPES---FTVHGQGMVGPVPVPVIYMAVIGVIA-HI 176 TL LS+GR LA V++ F + G G +P V+Y V GVI H Sbjct: 141 VTLATLSIGRSLALVLTNNEVFYEFGRATNGIIALGGGYSFGLP-NVVYALVAGVIILHF 199 Query: 177 FLKYTVTGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPN 236 L T GR ++AIGGN A++L GI D I + Y NG + A L WLG Sbjct: 200 LLTMTRWGRYLFAIGGNEAAARLAGIPVDLIKVSAYAFNGLMVAITAVFLVGWLGAVTNA 259 Query: 237 AGQGYELDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGI 296 G GYEL VIA+TVIGG SL+GG GT LGA +GA+++ V+RN +++ GV+ FWQ + +G Sbjct: 260 IGTGYELQVIASTVIGGASLTGGFGTALGAAIGAILVEVIRNALLIAGVNPFWQGMFVGS 319 Query: 297 VIIIAIAIDQIR 308 I+ A+ +++IR Sbjct: 320 FILAAVLLERIR 331 Lambda K H 0.328 0.145 0.421 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: 296 Number of extensions: 16 Number of successful extensions: 3 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: 313 Length of database: 335 Length adjustment: 28 Effective length of query: 285 Effective length of database: 307 Effective search space: 87495 Effective search space used: 87495 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 (21.7 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