Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate Dsui_0564 Dsui_0564 molybdenum ABC transporter, ATP-binding protein
Query= SwissProt::P19566 (369 letters) >FitnessBrowser__PS:Dsui_0564 Length = 365 Score = 142 bits (357), Expect = 2e-38 Identities = 90/210 (42%), Positives = 125/210 (59%), Gaps = 10/210 (4%) Query: 12 AWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIGETRMND-- 69 A+G+ ++ D+ L G +F G SG GK+TLLR IAGLE L + D Sbjct: 19 AYGEFSLAADLTLPGR-GVTALF-GHSGSGKTTLLRAIAGLERHPGAYLEVNGEVWQDGD 76 Query: 70 --IPPAERGVGMVFQSYALYPHLSVAENMSFGLK-LAGAKKEVMNQRVNQVAEVLQLAHL 126 +P R +G VFQ +L+PHLSV N+ FG K LA A++ V + Q E+L + HL Sbjct: 77 HFLPTHRRPLGYVFQEASLFPHLSVEANLDFGRKRLAAAERRV---DLAQAVELLGIGHL 133 Query: 127 LERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRT 186 L R+P LSGG+RQRVAI R L+A PR+ L+DEPL+ LD + ++ ++RL + L Sbjct: 134 LARRPDKLSGGERQRVAIARALLASPRLLLMDEPLAALDGKRKAEILPYLTRLREELDIP 193 Query: 187 MIYVTHDQVEAMTLADKIVVLDAGRVAQVG 216 ++YVTH E LAD +V+LD G+VA G Sbjct: 194 VLYVTHSPDEVARLADHLVLLDNGQVAASG 223 Lambda K H 0.321 0.138 0.396 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: 309 Number of extensions: 12 Number of successful extensions: 3 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: 369 Length of database: 365 Length adjustment: 30 Effective length of query: 339 Effective length of database: 335 Effective search space: 113565 Effective search space used: 113565 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: 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