Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Koxy:BWI76_RS03270 Length = 376 Score = 333 bits (854), Expect = 4e-96 Identities = 183/371 (49%), Positives = 247/371 (66%), Gaps = 22/371 (5%) Query: 1 MAPVTLKKLVKRY-GALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGA 59 MA V+L+K+ KRY + VHGIDLE+ D EF+ VGPSGC KSTTLRMIAGLE++SGG Sbjct: 1 MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60 Query: 60 IEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119 I IG RKVNDLPP+ R I+MVFQ+YALYPH TV +NM F LK+ RP +EIK RV +AA Sbjct: 61 IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 L++ LL R+P ++SGGQRQRVA+GRAIVR+PDVFLFDEPLSNLDAKLR +R +I +L Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180 Query: 180 HARMQ-----ATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFI 234 H ++ ATMIYVTHDQ EA+TL DRI ++ G+I QV TP D++ P KFVA FI Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240 Query: 235 GSPPMNMEEAVLTDGK----LAFASGATLPLPPRFRSLVREG---QKVTFGLRPDDVYPS 287 GSP +N+ + + + A G + L P + ++ EG + V FG+RP+ Sbjct: 241 GSPSINLIDTAIRKNNERLYVEIAPGVEI-LIPHSKQVLLEGYINKPVCFGIRPE----- 294 Query: 288 GHGLHAGDADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRM--LNPRPLRPGEAVPM 345 H A D D ++ E +T+ E +G+E ++ G++ ++R+ + P G+ + Sbjct: 295 -HISLASDDDDLNTFEGVLTVVENMGSEKFLYFIVGGKELIARVDTQDINPFHIGKTLRF 353 Query: 346 SFDLARAHLFD 356 + + A H+FD Sbjct: 354 NLNTAFCHVFD 364 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: 16 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: 376 Length adjustment: 30 Effective length of query: 335 Effective length of database: 346 Effective search space: 115910 Effective search space used: 115910 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