Align ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized)
to candidate HSERO_RS01340 HSERO_RS01340 sugar ABC transporter permease
Query= TCDB::G4FGN7 (293 letters) >FitnessBrowser__HerbieS:HSERO_RS01340 Length = 311 Score = 138 bits (347), Expect = 2e-37 Identities = 86/287 (29%), Positives = 146/287 (50%), Gaps = 15/287 (5%) Query: 4 RSGWTAFWMILPTILVISVVAFFPLFKTFYDSFYSF-GLRPGIERRFVGLQNYFRLFEDT 62 R AFW + P ++ V +P+ T Y SF+S+ G+ E RFVGL NY LF Sbjct: 33 RRNRAAFWFLAPACVMTLVYVLYPILYTIYLSFFSWDGMT---EPRFVGLANYVELFHAP 89 Query: 63 RFIMALKNTVFFTVISVSLETVLGVLIAIVVHQRFALRGVVRAAMLVPWAIPTAISSQMW 122 F ALKN V + ++ + L +G+ IA+ ++Q+ VV++ P+ + + M+ Sbjct: 90 TFYTALKNNVLWLLMFL-LAPPMGLAIALYLNQKVIGMRVVKSLFFAPFVLSGVVVGLMY 148 Query: 123 RWMFHDQFGIMSRLWEKLGIIEPGTPILGTPGLAMWAIIFVDVWKTTPFMALLILAGLQV 182 W + FG++S L+ + G P+LG A + IIF +W T + +L L GL Sbjct: 149 SWFYDPSFGLLSLLFGQ------GVPVLGDARYATFGIIFAALWPQTAYCMILFLTGLTA 202 Query: 183 IPEDIYEAARIDGANTIQRFFRITLPLITPTIGVALIFRTLDALRVFDVVYIMTRGA-VN 241 + D EAAR++GA + LP + T +A + + ALR FD++ +MT G Sbjct: 203 LNHDQVEAARMEGAKGWTMLRYVILPQLRSTTFMAFVVSIIGALRSFDLISVMTSGGPYE 262 Query: 242 TETLAVYNRHVLMDRAFTGAWFGYGSAISVFIFVLISVFAILYIKSL 288 + T+ Y + D+A GY +A++V +F ++ V+ + ++ + Sbjct: 263 SSTVLAYYAY---DQAIKYYRQGYSAAVAVTLFAIMLVYIVYQLRRM 306 Lambda K H 0.333 0.145 0.457 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: 273 Number of extensions: 20 Number of successful extensions: 4 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: 293 Length of database: 311 Length adjustment: 27 Effective length of query: 266 Effective length of database: 284 Effective search space: 75544 Effective search space used: 75544 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (21.5 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