Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, 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 Ga0059261_1321 Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__Korea:Ga0059261_1321 Length = 238 Score = 103 bits (256), Expect = 6e-27 Identities = 71/226 (31%), Positives = 108/226 (47%), Gaps = 17/226 (7%) Query: 4 VRLEHVWKRFGKVV----AVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGN 59 +RL ++ K FG+ A+K +L+ + +FV +GPSG GK+TT+ ++ L+ + G Sbjct: 8 IRLRNITKVFGEGATAFQALKGVDLDIAERDFVAVMGPSGSGKSTTMNILGCLDVPTSGE 67 Query: 60 IYIGDRLVNDVPPKDRD---------IAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEI 110 + + DRD + VFQ + L N EN+ L R K Sbjct: 68 FLFKGVYIETL---DRDQRALVRRKYLGFVFQGFNLLSRTNALENVELPLLYRGEDKKVR 124 Query: 111 DRRVKEAARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRV 170 A + + + P ELSGGQ QRVA+ RAIV P V L DEP NLD+ V Sbjct: 125 HELGMAALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPAVLLADEPTGNLDSARSV 184 Query: 171 EMRAEIAKLQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVD 216 E+ + L + G+T + VTH+ + IV KDG +++ + Sbjct: 185 EIMELLTSLNKDSGITVLMVTHEP-DMAAFARTIVHFKDGLVERTE 229 Lambda K H 0.320 0.139 0.400 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: 189 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: 376 Length of database: 238 Length adjustment: 27 Effective length of query: 349 Effective length of database: 211 Effective search space: 73639 Effective search space used: 73639 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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