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 209225 DVU0291 ABC transporter, ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >MicrobesOnline__882:209225 Length = 354 Score = 150 bits (380), Expect = 4e-41 Identities = 88/232 (37%), Positives = 124/232 (53%), Gaps = 20/232 (8%) Query: 21 VENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMNDASPKDRDIA 80 + + NL E + VGPSG GK+T LR IAGL+ EG + + + + Sbjct: 18 LHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTIRVTPPQGHGGG-----VV 72 Query: 81 MVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL-----GLTEFLERKPAD 135 +VFQ+Y L+PH+SV+EN+AFG + R + + +RVH L R PA Sbjct: 73 LVFQDYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRAFRLDTDDLAHMASRYPAQ 132 Query: 136 LSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVTHD 195 LS GQRQRVA+ RA+V D V L+DEP +NLD LR M A + + RR G T+ VTHD Sbjct: 133 LSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFVRDVVRRFGVATVTVTHD 192 Query: 196 QTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIG 247 EA + DR+ +M G + Q+ P ++Y PA++ A F+G Sbjct: 193 LEEAFAIGDRLGVMLG----------GTLAQLAPPLDVYRHPADEATARFLG 234 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: 296 Number of extensions: 14 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: 377 Length of database: 354 Length adjustment: 30 Effective length of query: 347 Effective length of database: 324 Effective search space: 112428 Effective search space used: 112428 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: 49 (23.5 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