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 WP_049989937.1 LT39_RS07855 sugar ABC transporter permease
Query= TCDB::Q72H67 (291 letters) >NCBI__GCF_000784335.1:WP_049989937.1 Length = 308 Score = 178 bits (452), Expect = 1e-49 Identities = 99/282 (35%), Positives = 158/282 (56%), Gaps = 8/282 (2%) Query: 11 WILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPDFRQALW 70 ++ ++P +++V + YP+AQ Y SFF + + EFVGL NY ++ +PD Q LW Sbjct: 25 YLPIVPVMVLVGVFILYPIAQAIYSSFFDKSLLSPDEAEFVGLANYQEIWTNPDLHQVLW 84 Query: 71 NTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQWMLNDV 130 NT + V V G + +++ F + +LIPW +P VV A +WQ+M Sbjct: 85 NTFVWVSVGSIAAIVFGFVLGWLLYEKFPYTSVASAIVLIPWVLPRVVGASIWQFMFGGD 144 Query: 131 YGVINVLGVKLGLLSQKVAFLARPEL-LLPSIIAVDVWKTTPFMALLLLAGLQMIPEELY 189 G+IN L V+LG++ + + L +L L P II + +W+ P ALL L LQ I E LY Sbjct: 145 QGIINELLVQLGVIDEYMVMLGSGDLSLWPPIIGM-IWRLAPLFALLTLTSLQGIDEHLY 203 Query: 190 EAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMS----GVNPATRT 245 EAA +DGA+ W++F ITLP++ L + + + +R F +V+VM+ GV+ +T Sbjct: 204 EAARMDGATPWERFRYITLPMMRYNLAIGFLLMLIYNIRNFSMVWVMTEGGPGVSSSTLP 263 Query: 246 LAVYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMRTVGK 287 + +Y R VDF ++G SA+SV + V++ F Y++ K Sbjct: 264 VMIY-RTAFVDF-NVGLASALSVLLFVVLLVFSYYYIKVYDK 303 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: 252 Number of extensions: 9 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: 291 Length of database: 308 Length adjustment: 27 Effective length of query: 264 Effective length of database: 281 Effective search space: 74184 Effective search space used: 74184 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 24 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