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_086511009.1 BZY95_RS16610 sugar ABC transporter permease
Query= TCDB::Q72H67 (291 letters) >NCBI__GCF_002151265.1:WP_086511009.1 Length = 310 Score = 146 bits (369), Expect = 5e-40 Identities = 86/279 (30%), Positives = 144/279 (51%), Gaps = 5/279 (1%) Query: 12 ILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPDFRQALWN 71 IL+ P L++ L PLA Y+S F + + P FVG +NY L F ALWN Sbjct: 32 ILLPPALILFSLFVILPLADAAYYSAFSWN-GYGTPTNFVGTQNYERLLDHSVFHTALWN 90 Query: 72 TLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQWMLNDVY 131 T K +VS+ ++ L L +AL+++ L R +P+ + V + +W ++ + Y Sbjct: 91 TAKLILVSLIIQMPLALGLALLVYRKTPTNTLFRLVFFLPYILAEVAAGLIWSFVFDGDY 150 Query: 132 GVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMIPEELYEA 191 G+ + LG + V LA + P+I+ V VWK F ++ +A LQ +P++L EA Sbjct: 151 GITAFMFQTLG--QESVYVLADRQWAFPAIMTVIVWKYFGFHMMIYIAALQSVPKDLIEA 208 Query: 192 ASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNP--ATRTLAVY 249 A ++GA Q + +PL+ A+VV+ F + +L++FD++ M+ P +T T+ Y Sbjct: 209 AKLEGAKPRQVALFVQIPLIKHAIVVSGFFAIIGSLQIFDIIIPMTNGGPSNSTHTIVTY 268 Query: 250 NRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMRTVGKE 288 + ++G+GSA +V + V+ L Y R KE Sbjct: 269 LYTFGLSRLNIGFGSAAAVVLFVLAIGIALFYQRATAKE 307 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: 220 Number of extensions: 10 Number of successful extensions: 4 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: 310 Length adjustment: 27 Effective length of query: 264 Effective length of database: 283 Effective search space: 74712 Effective search space used: 74712 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