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 SMa0710 SMa0710 ABC transporter permease
Query= TCDB::Q72H67 (291 letters) >FitnessBrowser__Smeli:SMa0710 Length = 337 Score = 189 bits (479), Expect = 1e-52 Identities = 101/281 (35%), Positives = 161/281 (57%), Gaps = 3/281 (1%) Query: 5 RQVRLAWILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEF-VGLENYAYLFQDP 63 RQ L ++L+LP + +V L+ YPL SF K +A + P LENY LF P Sbjct: 49 RQHWLGYLLLLPAVALVALIIVYPLFVSLDLSFQKIGMATLSAPRKPFTLENYHKLFASP 108 Query: 64 DFRQALWNTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMW 123 DF + W T+K VV + +GL AL++++ F+GR L R + +PWA+P V++ ++ Sbjct: 109 DFWNSCWVTIKLVVVVSAACFAVGLGTALLVNNRFKGRTLARLFVALPWAVPEVIAVVIF 168 Query: 124 QWMLNDVYGVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQM 183 W+ + +G++N L +KLG+ SQ + + + P + +WK PF++++ LAGLQ Sbjct: 169 AWIFDSSFGLMNWLFIKLGITSQMINWFSEPTAAFWVVAITMIWKGYPFVSIMTLAGLQS 228 Query: 184 IPEELYEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNP-- 241 IPE+ Y AA +DGA+ +Q+FW IT+P+L P L V + L R F ++ V++ P Sbjct: 229 IPEDFYNAAKVDGANAFQRFWYITIPVLMPVLGVTSVLVVLWVFRDFSIIKVLTDGGPLK 288 Query: 242 ATRTLAVYNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYM 282 AT+TL++ F ++GY SAI + LV+ LL + Sbjct: 289 ATQTLSIMTYDQAFGFFNMGYASAIGIVTLVLCVVASLLML 329 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: 266 Number of extensions: 10 Number of successful extensions: 2 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: 337 Length adjustment: 27 Effective length of query: 264 Effective length of database: 310 Effective search space: 81840 Effective search space used: 81840 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