Align Maltose transport system permease protein malF aka TT_C1628, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate GFF726 PGA1_c07410 binding protein dependent transport system permease
Query= TCDB::Q72H67 (291 letters) >FitnessBrowser__Phaeo:GFF726 Length = 315 Score = 142 bits (357), Expect = 1e-38 Identities = 85/282 (30%), Positives = 147/282 (52%), Gaps = 9/282 (3%) Query: 5 RQVRLAWILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPD 64 RQ W+ + P ++ + +P+ Q F SF++ D + P+F+G+ENY L D Sbjct: 28 RQALAPWLFLAPGVIFFLFYVIFPILQSFNLSFYRWD--GLGDPQFIGMENYRELMDDRA 85 Query: 65 FRQALWNTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQ 124 F +LWN LK+ ++ + L GL IAL ++ G L ++ P+ I VV ++ Sbjct: 86 FEVSLWNNLKWLLLYL-LAIPAGLFIALFLNQTVTGIRLYKSLFFFPFVISQVVVGLVFS 144 Query: 125 WMLNDVYGVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMI 184 W + +G++N + +GL + L P L+ II +W T + +L L GL + Sbjct: 145 WFYDPTFGLLNQVLAWVGL--GPINVLGDPTLVTYGIIIAGLWPQTAYCMILYLTGLNAV 202 Query: 185 PEELYEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNP--A 242 E EAA +DGA + W + +P L PA VA + + ALR FD++ +M+ P + Sbjct: 203 DPEQVEAARLDGAKGAKMLWYVIIPQLRPATFVAFVVTIIGALRSFDLISIMTNGGPFGS 262 Query: 243 TRTLAVYN-RQTLVDFQ-DLGYGSAISVAILVIIFAFVLLYM 282 +R L+ Y + L ++ +GYG+AI+V + +I+ F+ ++ Sbjct: 263 SRVLSFYMFEKALSEYGFRMGYGAAIAVVLFLIMLCFIAYFL 304 Lambda K H 0.329 0.142 0.433 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: 277 Number of extensions: 16 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: 291 Length of database: 315 Length adjustment: 27 Effective length of query: 264 Effective length of database: 288 Effective search space: 76032 Effective search space used: 76032 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