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 HSERO_RS15495 HSERO_RS15495 ABC transporter permease
Query= TCDB::Q72H67 (291 letters) >FitnessBrowser__HerbieS:HSERO_RS15495 Length = 291 Score = 166 bits (420), Expect = 6e-46 Identities = 94/281 (33%), Positives = 148/281 (52%), Gaps = 5/281 (1%) Query: 9 LAWILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPDFRQA 68 L W+L+ P +++++ YP + SFF V P FVGLENY + DP F QA Sbjct: 9 LPWLLLSPAMVLLIAFTHYPALATLWHSFFSTPKG-VRPSVFVGLENYRLMADDPVFWQA 67 Query: 69 LWNTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQWMLN 128 L N L F + ++ L L + +AL ++ GRG++R A P +P + A +W + Sbjct: 68 LCNNLWFALGTIPLAIALAILMALWVNEKLAGRGVLRLAYFTPTVLPMIAVANIWLFFYT 127 Query: 129 DVYGVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMIPEEL 188 YG++ + LGL S +L P+ +L +++ V VWK F + LA LQ I L Sbjct: 128 PQYGLLEQITGALGLPSHN--WLGNPQTVLGALMVVAVWKEAGFFMIFYLAALQQISPVL 185 Query: 189 YEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMS--GVNPATRTL 246 EAA+++GASRWQ FW + PLL P + LI ++A R+ D + VM+ G + A+ L Sbjct: 186 AEAAALEGASRWQYFWRVQFPLLMPTTLFVLINALINAFRLVDHIVVMTKGGPDNASSLL 245 Query: 247 AVYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMRTVGK 287 Y + F D Y +A++V +L ++ L+ R + + Sbjct: 246 LYYIYEVGFAFWDSSYAAALTVVLLALLGLIALVKFRVLDR 286 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: 236 Number of extensions: 13 Number of successful extensions: 3 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: 291 Length adjustment: 26 Effective length of query: 265 Effective length of database: 265 Effective search space: 70225 Effective search space used: 70225 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