Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 310 bits (793), Expect = 5e-89 Identities = 179/365 (49%), Positives = 232/365 (63%), Gaps = 20/365 (5%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 MA + L+ + K +G + GIDL ++ EFI VGPSGCGKST LR+IAGLE + GG++ Sbjct: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 + GR + D P R+++MVFQSYALYPHM+V ENM F+LK+A + I +V AA I Sbjct: 61 MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 L+L L+R P +LSGGQRQRVA+GRAIVR P VFLFDEPLSNLDA LR Q R EI KLH Sbjct: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240 + AT IYVTHDQVEAMTL+DR+V++RDG IEQVGTP +++ +PA +FVA FIG+P MN Sbjct: 181 RDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMN 240 Query: 241 MEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAVH 300 V+ KL P P ++ GLRP+++ G Sbjct: 241 ----VVPVDKLPQPVQQQAPAAPAGAAV------GAIGLRPENITVRTTG--------AT 282 Query: 301 EIELPVTITEPLGNETLVF-TQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLFDGET 359 + V + E LG ETL++ T G +VSR + LR G+AV + D ++AH FD Sbjct: 283 PVGGQVDLIEALGAETLIYVTTPGGAQFVSRQNDRTDLRVGDAVSLDIDASQAHWFD-TA 341 Query: 360 GRALA 364 GR +A Sbjct: 342 GRVVA 346 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: 341 Number of extensions: 10 Number of successful extensions: 2 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: 350 Length adjustment: 29 Effective length of query: 336 Effective length of database: 321 Effective search space: 107856 Effective search space used: 107856 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