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_RS16725 HSERO_RS16725 ABC transporter permease
Query= TCDB::G4FGN7 (293 letters) >FitnessBrowser__HerbieS:HSERO_RS16725 Length = 299 Score = 168 bits (425), Expect = 2e-46 Identities = 93/267 (34%), Positives = 155/267 (58%), Gaps = 6/267 (2%) Query: 15 PTILVISVVAFFPLFKTFYDSFYSFGLRPGIERRFVGLQNYFRLFEDTRFIMALKNTVFF 74 P ++++ V +PL + F + G E F+GL N+ L D+ ++L NTVF+ Sbjct: 19 PAVILLVVFLTYPLGLGIWLGFTDTKI--GGEGSFIGLDNFTYLAGDSLAQLSLFNTVFY 76 Query: 75 TVISVSLETVLGVLIAIVVHQRFALRGVVRAAMLVPWAIPTAISSQMWRWMFHDQFGIMS 134 TV + L+ +LG+ +AI++++ L+ RA +L+PW +PTA+S+ + W++ QF ++S Sbjct: 77 TVSASILKFMLGLWLAILLNKNVPLKTFFRAIVLLPWIVPTALSALAFWWLYDAQFSVIS 136 Query: 135 RLWEKLGIIEPGTPILGTPGLAMWAIIFVDVWKTTPFMALLILAGLQVIPEDIYEAARID 194 K+G+I+ LG P A W+ +F +VW+ PF+A+ +LAGLQ I +YEAA ID Sbjct: 137 WALHKMGLIDRYIDFLGDPWNARWSTVFANVWRGIPFVAISLLAGLQTISPSLYEAAAID 196 Query: 195 GANTIQRFFRITLPLITPTIGVALIFRTLDALRVFDVVYIMTRGAVNTETLAVYNRHVLM 254 GA Q+F +TLPL+TP I V + F L F ++Y++TRG T + + Sbjct: 197 GATPWQQFRHVTLPLLTPIIAVVMTFSVLFTFTDFQLIYVLTRGGPLNATHLMAT--LSF 254 Query: 255 DRAFTGAWFGYGSAISVFI--FVLISV 279 RA G G G+A++ ++ F+L ++ Sbjct: 255 QRAIPGGALGEGAALATYMIPFLLAAI 281 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: 320 Number of extensions: 18 Number of successful extensions: 1 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: 299 Length adjustment: 26 Effective length of query: 267 Effective length of database: 273 Effective search space: 72891 Effective search space used: 72891 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