Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate N515DRAFT_2307 N515DRAFT_2307 molybdate/tungstate transport system ATP-binding protein
Query= SwissProt::P19566 (369 letters) >FitnessBrowser__Dyella79:N515DRAFT_2307 Length = 331 Score = 122 bits (306), Expect = 1e-32 Identities = 79/205 (38%), Positives = 115/205 (56%), Gaps = 13/205 (6%) Query: 31 FVVFVGPSGCGKSTLLRMIAGLETITSGDLFIGETRMNDIPPAERGVGMVFQSYALYPHL 90 F V +G SG GK+ LL IAGL G+ F G +PP +R VG + Q +AL+PHL Sbjct: 22 FTVLLGASGEGKTLLLSAIAGL-IAARGEPFDG------LPPQQRAVGYLPQGHALFPHL 74 Query: 91 SVAENMSFGLKLAGAKKEVMNQRVNQVAEVLQLAHLLERKPKALSGGQRQRVAIGRTLVA 150 EN++F L+ A +++ M Q E + +A L ER P +LSGGQ+QRVA+ R L Sbjct: 75 RAWENVAFSLRGARRREQAM-----QWLERVGMAGLAERWPASLSGGQQQRVALARALAR 129 Query: 151 EPRVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAG 210 P + LLDEP S LD R ++ E+ + G + V+HD A +AD++V++ Sbjct: 130 RPSLLLLDEPTSALDPVTRDEVLAELIAEVHQAGIPALAVSHDPALA-AVADRLVLMHGR 188 Query: 211 RVAQVGKPLELYHYPADRFVAGFIG 235 R+ Q+G P ++ PA VA +G Sbjct: 189 RIVQIGTPEAVHAQPASGAVARLLG 213 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: 310 Number of extensions: 22 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: 369 Length of database: 331 Length adjustment: 29 Effective length of query: 340 Effective length of database: 302 Effective search space: 102680 Effective search space used: 102680 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