Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_900167125.1:WP_200806763.1 Length = 406 Score = 235 bits (600), Expect = 1e-66 Identities = 142/348 (40%), Positives = 205/348 (58%), Gaps = 10/348 (2%) Query: 4 VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63 V L+ L+KR+G V DL ++ E + L+GPSGCGK+T LRMIAGLE + G I I Sbjct: 45 VRLQGLMKRFGKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYIK 104 Query: 64 GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDL 123 GR++ND P RN+ M+FQ+YAL+PH T+ EN+ F LK EE++ +VA+A ++ L Sbjct: 105 GRRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVRL 164 Query: 124 AHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARM 183 + +R SQLSGGQ+QR+A+ RAIV +PDV L DEPLS LD KLR ++R EI + ++ Sbjct: 165 PGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQL 224 Query: 184 QATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEE 243 T ++VTHDQ EA+++S++IV+M+DG +Q GTPEDV+ P FVA F+G N + Sbjct: 225 NLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGH--ANFFD 282 Query: 244 A----VLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAV 299 A VL + ++ L R+GQ V +R + + L + ++ Sbjct: 283 ARVLEVLDNDQVRVRIAEGLEFTADHVGRWRQGQDVHLVMRAQKINVTSPDLADEELEST 342 Query: 300 HEIELPVTITEP--LGNETLVFTQF-NG-RDWVSRMLNPRPLRPGEAV 343 P I + +G ET F + NG R + M+ RP R G+ V Sbjct: 343 DLNYYPGKIYDRSYMGGETSYFVELANGVRLHIISMVRRRPHRIGDEV 390 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: 359 Number of extensions: 14 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: 406 Length adjustment: 30 Effective length of query: 335 Effective length of database: 376 Effective search space: 125960 Effective search space used: 125960 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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