Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__HerbieS:HSERO_RS22750 Length = 377 Score = 329 bits (843), Expect = 8e-95 Identities = 189/372 (50%), Positives = 242/372 (65%), Gaps = 21/372 (5%) Query: 1 MAPVTLKKLVKRY-GALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGA 59 MA V +K+L K Y G +V+ G++L+++D EF LVGPSGCGKST LRM+ GLEE+SGG Sbjct: 1 MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60 Query: 60 IEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119 + IGG+ VN LPP R I+MVFQSYALYPHM V +NM F LK+AG +I R+ AAA Sbjct: 61 LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAA 120 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 IL + HLL+R P +LSGGQRQRVA+GRAIVRQP +FLFDEPLSNLDA LR Q R EI KL Sbjct: 121 ILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKL 180 Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPM 239 H ++ AT++YVTHDQVEAMTL D+IV+M +G I+Q GTP +++++P FVAGFIGSP M Sbjct: 181 HRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPKM 240 Query: 240 NMEEAVLTDGKLAFASGATLPLPPRFRSL-------VREGQKVTFGLRPDDVYPSGHGLH 292 N + V+T SG + + R L V G VT GLR + + GL Sbjct: 241 NFFQGVVT---RCDDSGVQVEIAGGLRLLADVDPLGVTPGAAVTLGLRAEQI---REGL- 293 Query: 293 AGDADAVHEIELPVTITEPLGNETLVF-TQFNGRDWVSRMLNPRPLRPGEAVPMSFDLAR 351 GD +H + V + E LG ++ T G D V R R + G+ + +S Sbjct: 294 -GDGQPLHGV---VNLVEHLGEANFLYVTLDGGHDIVVRGDGNRNVDIGQPIALSVHSHA 349 Query: 352 AHLFDGETGRAL 363 HLFD + G+AL Sbjct: 350 FHLFDAQ-GQAL 360 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: 412 Number of extensions: 13 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: 377 Length adjustment: 30 Effective length of query: 335 Effective length of database: 347 Effective search space: 116245 Effective search space used: 116245 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