Align TreV, component of Trehalose porter (characterized)
to candidate N515DRAFT_2307 N515DRAFT_2307 molybdate/tungstate transport system ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Dyella79:N515DRAFT_2307 Length = 331 Score = 117 bits (293), Expect = 4e-31 Identities = 73/209 (34%), Positives = 118/209 (56%), Gaps = 13/209 (6%) Query: 26 ETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPEKRNVAMVFQNYAL 85 E F V+LG SGEGK+ LL +AG+ I A G PP++R V + Q +AL Sbjct: 18 EVAGFTVLLGASGEGKTLLLSAIAGL-------IAARGEPFDGLPPQQRAVGYLPQGHAL 70 Query: 86 YPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKVTQISGGQQQRVALAR 145 +P++ +N+AF L+ ++E+ ++ +E+ +G++ + ++ +SGGQQQRVALAR Sbjct: 71 FPHLRAWENVAFSLR-GARRREQAMQWLER----VGMAGLAERWPASLSGGQQQRVALAR 125 Query: 146 AIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVTHDQKEALSLADRIAI 205 A+ R PS LLDEP S LD R EL + + V+HD A ++ADR+ + Sbjct: 126 ALARRPSLLLLDEPTSALDPVTRDEVLAELIAEVHQAGIPALAVSHDPALA-AVADRLVL 184 Query: 206 LHKGKFEQVSDPKTLYEYPKTKWVAQFVG 234 +H + Q+ P+ ++ P + VA+ +G Sbjct: 185 MHGRRIVQIGTPEAVHAQPASGAVARLLG 213 Lambda K H 0.318 0.137 0.385 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: 210 Number of extensions: 9 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: 324 Length of database: 331 Length adjustment: 28 Effective length of query: 296 Effective length of database: 303 Effective search space: 89688 Effective search space used: 89688 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