Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_000007345.1:WP_011020381.1 Length = 353 Score = 186 bits (473), Expect = 6e-52 Identities = 102/304 (33%), Positives = 169/304 (55%), Gaps = 10/304 (3%) Query: 21 GIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVNDLPPRARNISMV 80 GIDL + +++AL+GPSG GKS L I G G++ + GR + P R IS+V Sbjct: 20 GIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQGSVFLEGRDITFFSPDKRQISIV 79 Query: 81 FQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDLAHLLERRPSQLSGGQRQ 140 +Q L+PHM + EN+ ++L+ + ++I+ V + A +L + LL R+P LSGG++Q Sbjct: 80 YQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIAGVLGIRELLHRKPDTLSGGEKQ 139 Query: 141 RVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVTHDQVEAMTL 200 R ++ R++V +P + L DEP S LDA+ R ++R +KK A T+++VTHD + L Sbjct: 140 RASLARSLVARPKLLLLDEPFSALDARTREKLREMLKKAIADYSTTVLHVTHDFEDVWAL 199 Query: 201 SDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEEAVLTDGKLAFASGATLP 260 ++R+V++R G + QVG PE VFRRP+ FVA F+G+ + L +GKL + Sbjct: 200 ANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGTNVLKGTVKAL-EGKLTVIDAEGME 258 Query: 261 LPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHA-------GDADAVHEIELPVTITEPLG 313 + G+ VT +RP+++ +G + + G + + E V + +G Sbjct: 259 I--YSADPAEPGENVTVSIRPEEIILAGGTVESSARNTLKGRVSGIFKKEHLVVVEVKMG 316 Query: 314 NETL 317 N + Sbjct: 317 NSEI 320 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: 318 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: 353 Length adjustment: 29 Effective length of query: 336 Effective length of database: 324 Effective search space: 108864 Effective search space used: 108864 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 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