Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate BWI76_RS23390 BWI76_RS23390 oligogalacturonide ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Koxy:BWI76_RS23390 Length = 375 Score = 317 bits (811), Expect = 4e-91 Identities = 180/375 (48%), Positives = 241/375 (64%), Gaps = 22/375 (5%) Query: 1 MAPVTLKKLVKRYG-ALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGA 59 MA V KL K Y + VHGIDL++ D EF+ +VGPSGC KSTTLRM+AGLE +SGG Sbjct: 1 MAEVIFNKLEKVYSNGFKAVHGIDLKIADGEFMVIVGPSGCAKSTTLRMLAGLETISGGE 60 Query: 60 IEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119 + IG + VN+L P+AR I+MVFQ+YALYPHMTV EN+ F LK++ P ++I+ +V EAA Sbjct: 61 VRIGEKIVNNLAPKARGIAMVFQNYALYPHMTVRENLAFGLKLSKLPKDQIEAQVNEAAK 120 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 IL+L LL+R P QLSGGQ QRVA+GRAIV++PDVFLFDEPLSNLDAKLR +R I L Sbjct: 121 ILELEELLDRLPRQLSGGQAQRVAVGRAIVKKPDVFLFDEPLSNLDAKLRASMRIRISDL 180 Query: 180 HARMQ-----ATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFI 234 H +++ AT +YVTHDQ EAMT+ DRI +M+ GHI QV TP++++ +P FVAGFI Sbjct: 181 HKQLKKSGKPATTVYVTHDQTEAMTMGDRICVMKLGHIMQVDTPDNLYHKPKNMFVAGFI 240 Query: 235 GSPPMNMEEAVLTD--GKLAFASG-ATLPLPPRFRSLV--REGQKVTFGLRPDDVYPSGH 289 G+P MN+ + L + G+L G LPL R +S V + Q+V FG+RP+ V S Sbjct: 241 GAPEMNIRPSQLVEQAGRLHLTVGDGLLPLNDRLQSKVDTHKNQQVFFGVRPEFVSISDE 300 Query: 290 GLHAGDADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRP---LRPG--EAVP 344 G + E +G+E V+ + + +R+ + + G V Sbjct: 301 PFAEGSCTG------EMVRVENMGHEFFVYLKVADYELTARVPSDEAKPMIEKGLHRKVH 354 Query: 345 MSFDLARAHLFDGET 359 FDL + H+FD +T Sbjct: 355 FKFDLNKCHIFDAKT 369 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: 369 Number of extensions: 14 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: 375 Length adjustment: 30 Effective length of query: 335 Effective length of database: 345 Effective search space: 115575 Effective search space used: 115575 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