Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Cola:Echvi_3653 Length = 290 Score = 149 bits (375), Expect = 1e-40 Identities = 94/253 (37%), Positives = 141/253 (55%), Gaps = 14/253 (5%) Query: 1 MAPVTLKKLVKRYG-ALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGA 59 M + L+K +K G A+++ I L + EFI L GPSG GK++TLRMI+GL G Sbjct: 1 MINIDLQKSLKANGPAMDL--DIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGH 58 Query: 60 IEIGGRKVND------LPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTR 113 + + G + D + P R + +FQ Y+L+P+MTV EN+ F+LK A + K Sbjct: 59 LSVNGEQWFDASFGKNVSPGRRKLGYLFQDYSLFPNMTVKENIAFALKNA-----KDKAY 113 Query: 114 VAEAAAILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVR 173 + E + L HL + P LSGGQ+QRVA+ RA+ +PD+ L DEPLS LD +R +++ Sbjct: 114 LMELLESMGLLHLQDTLPKHLSGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQ 173 Query: 174 TEIKKLHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGF 233 I +H + T I V+HD E + LSDRI+ + G + + TP++ F T F Sbjct: 174 EYILAIHRKYALTTILVSHDAGEIIKLSDRIIELDHGKVLRQCTPKEFFGTGLTSAKFQF 233 Query: 234 IGSPPMNMEEAVL 246 G +E+ V+ Sbjct: 234 QGEIMDILEDDVV 246 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: 263 Number of extensions: 11 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: 365 Length of database: 290 Length adjustment: 28 Effective length of query: 337 Effective length of database: 262 Effective search space: 88294 Effective search space used: 88294 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: 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