Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 232 bits (591), Expect = 1e-65 Identities = 111/260 (42%), Positives = 171/260 (65%), Gaps = 2/260 (0%) Query: 4 VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63 + L+ + K + + IDL +++ EF+ L+GPSGCGK+T LR+++G E+ + G + I Sbjct: 8 IELRGVTKTFEDTVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVRIN 67 Query: 64 GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDL 123 G+ VN +PP R ++ VFQ+YAL+PHMTV +N+ F LK+ G A+E RV +A ++ L Sbjct: 68 GQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLDALRMVHL 127 Query: 124 AHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARM 183 + +R+P QLSGGQ+QRVA+ RA++ P V L DEP S LD KLR Q++ EIK L ++ Sbjct: 128 ENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKHLQRQL 187 Query: 184 QATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEE 243 T ++VTHDQ EA +SDR+V+M +G IEQ+G P++++ PA +VA F+G +N Sbjct: 188 GITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFVGD--INALP 245 Query: 244 AVLTDGKLAFASGATLPLPP 263 + +L +++ PL P Sbjct: 246 GRIDAVRLDWSAAPGTPLAP 265 Lambda K H 0.320 0.137 0.397 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: 372 Number of extensions: 15 Number of successful extensions: 1 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: 365 Length of database: 399 Length adjustment: 30 Effective length of query: 335 Effective length of database: 369 Effective search space: 123615 Effective search space used: 123615 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: 50 (23.9 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