Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate N515DRAFT_2307 N515DRAFT_2307 molybdate/tungstate transport system ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Dyella79:N515DRAFT_2307 Length = 331 Score = 110 bits (276), Expect = 4e-29 Identities = 77/223 (34%), Positives = 125/223 (56%), Gaps = 19/223 (8%) Query: 33 VFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTV 92 V +G SG GK+ LL IAGL + G + +PP QR + + Q +AL+PH+ Sbjct: 24 VLLGASGEGKTLLLSAIAGL-------IAARGEPFDGLPPQQRAVGYLPQGHALFPHLRA 76 Query: 93 RENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDP 152 EN++F+L+ A++ + + E++ + +R P +LSGGQ+QRVA+ R++ R P Sbjct: 77 WENVAFSLRGARRREQAMQWL-----ERVGMAGLAERWPASLSGGQQQRVALARALARRP 131 Query: 153 KVYLFDEPLSNLDAALRVATRLE-IAQLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGG 211 + L DEP S LD R E IA++ +A + V+HD A +A R+V++ G Sbjct: 132 SLLLLDEPTSALDPVTRDEVLAELIAEVHQA--GIPALAVSHDPALA-AVADRLVLMHGR 188 Query: 212 GIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGKIIGT-GAQ 253 I Q+G+P ++ +P + VA+ +G N+ G+I+G GAQ Sbjct: 189 RIVQIGTPEAVHAQPASGAVARLLG--LRNVQRGRIVGAPGAQ 229 Lambda K H 0.316 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: 274 Number of extensions: 15 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: 373 Length of database: 331 Length adjustment: 29 Effective length of query: 344 Effective length of database: 302 Effective search space: 103888 Effective search space used: 103888 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 (21.6 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