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 BPHYT_RS22740 BPHYT_RS22740 ABC transporter permease
Query= TCDB::G4FGN4 (313 letters) >FitnessBrowser__BFirm:BPHYT_RS22740 Length = 328 Score = 203 bits (517), Expect = 4e-57 Identities = 108/303 (35%), Positives = 178/303 (58%), Gaps = 7/303 (2%) Query: 10 EAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGS 69 E G + L+ F + FL+ +N+ ++ +A+++ G T++++T GIDLS G Sbjct: 23 EVGPLIALVLACGFFISQSSRFLSFQNLSLILQQTMVVAVIAIGQTLIVLTGGIDLSCGM 82 Query: 70 ILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVG 129 ++ S++M G+ P L+++ G+ FG NG+LIT+ +L FI TLG L++ Sbjct: 83 VMAFGSIIMTKFAVTLGVPPVLAILCGVGASALFGALNGVLITRIKLPAFIVTLGTLNIA 142 Query: 130 RGLAYVMSGGWPISPFPESFTVHGQGM-VGPVPVPVIYMAVIGVIAHI----FLKYTVTG 184 L + S +S P++ G +GP V Y V+ ++ ++ L+ TV G Sbjct: 143 FALTQIYSNAESVSNLPDAIMFLGNTFKLGPADVT--YGTVLTLLMYLATWFVLRDTVPG 200 Query: 185 RRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELD 244 R +YA+G N EA++L+G+ + +IL+ VY++ G + A L + GV P AGQ LD Sbjct: 201 RHLYALGNNPEAARLMGLSSQKILLTVYSLAGAIYGIAALLSVSRTGVGDPQAGQTENLD 260 Query: 245 VIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAI 304 I A V+GGTSL GG G+I G LGA+I+GV RNG+ L+GVSS +Q ++ G+++I+A+A Sbjct: 261 SITAVVLGGTSLFGGRGSISGTLLGALIVGVFRNGLTLIGVSSVYQVLITGMLVILAVAA 320 Query: 305 DQI 307 D++ Sbjct: 321 DKL 323 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: 248 Number of extensions: 11 Number of successful extensions: 2 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: 328 Length adjustment: 28 Effective length of query: 285 Effective length of database: 300 Effective search space: 85500 Effective search space used: 85500 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