Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Korea:Ga0059261_3874 Length = 243 Score = 101 bits (251), Expect = 2e-26 Identities = 69/206 (33%), Positives = 106/206 (51%), Gaps = 18/206 (8%) Query: 32 EFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMND-----ASPKDR----DIAMV 82 E + VGPSGCGKST L +++GL +G + D L N A +D + V Sbjct: 39 ELTLVVGPSGCGKSTLLAILSGLTLPDQGEV---DALGNPICRMKAGARDAFRLANTGFV 95 Query: 83 FQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLERKPADLSGGQRQ 142 FQ + L+ ++ E +A+ L+ K K + +R A E +GL + +P +LSGG++Q Sbjct: 96 FQGFNLFNALTAEEQVAYVLQCMKVKPAEARQRARAALEAVGLGPRMRLRPFELSGGEKQ 155 Query: 143 RVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVTHDQTEAMTL 202 RVA+ RA+ + ++ DEP S LD+ A+ A + I GA + VTHD ++ Sbjct: 156 RVAIARALAKQPRILFADEPTSALDSHNGHAVIALLRDIAHNQGAAVLCVTHD-PRLLSF 214 Query: 203 ADRIVIMS-----ATPNPDKTGSIGR 223 ADRI+ M PD T ++ R Sbjct: 215 ADRIIHMEDGRIIRDERPDPTSAVQR 240 Lambda K H 0.318 0.135 0.379 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: 161 Number of extensions: 12 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: 377 Length of database: 243 Length adjustment: 27 Effective length of query: 350 Effective length of database: 216 Effective search space: 75600 Effective search space used: 75600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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