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 AZOBR_RS18175 AZOBR_RS18175 sugar ABC transporter
Query= TCDB::Q72H67 (291 letters) >FitnessBrowser__azobra:AZOBR_RS18175 Length = 295 Score = 175 bits (444), Expect = 1e-48 Identities = 98/272 (36%), Positives = 148/272 (54%), Gaps = 2/272 (0%) Query: 12 ILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPDFRQALWN 71 + V P L +++ GYPL Q F S + +VGL+NY L DP+F Q L Sbjct: 10 LFVAPVALYLLVFQGYPLVQEFLLSVTSTSLLSPGQQTYVGLDNYRELVFDPEFHQVLRV 69 Query: 72 TLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQWMLNDVY 131 T +T+V V LGL AL++ FRGRG+ R + IPWA P V +A ++ WM N Y Sbjct: 70 TAVYTLVCVVASIGLGLLAALLLDGTFRGRGIARALVTIPWAAPPVAAALIFVWMFNAQY 129 Query: 132 GVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMIPEELYEA 191 G+ + L LG V +L P LP+I+ +W+ PF ++++LA LQ +P EL EA Sbjct: 130 GLFSHLAQFLGFAEGGVNWLDEPSFALPAILITTIWQIFPFSSVVILAALQGVPSELREA 189 Query: 192 ASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNP--ATRTLAVY 249 A IDGA R F ++T P + P++ + + T+ +LR FDV+++M+ P T TL + Sbjct: 190 AVIDGADRLSIFRAVTWPTIRPSVALLTLLITVWSLRRFDVIWLMTQGGPLGETNTLVID 249 Query: 250 NRQTLVDFQDLGYGSAISVAILVIIFAFVLLY 281 + + DLG +A+ + LV+ L+Y Sbjct: 250 LYRRAFVYLDLGRAAAVGIIGLVVAILVTLVY 281 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: 240 Number of extensions: 9 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: 295 Length adjustment: 26 Effective length of query: 265 Effective length of database: 269 Effective search space: 71285 Effective search space used: 71285 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