Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 144 bits (363), Expect = 2e-39 Identities = 85/229 (37%), Positives = 124/229 (54%), Gaps = 6/229 (2%) Query: 11 KRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVND- 69 K YG + + L+V E I + GPSG GKST +R I GLE G I IG +V Sbjct: 9 KWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVRPD 68 Query: 70 ---LPPRARNISMVFQSYALYPHMTVAENMGFS-LKIAGRPAEEIKTRVAEAAAILDLAH 125 L + MVFQ + L+PH+T+ EN + +K+ G + + E + +A Sbjct: 69 RRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIAD 128 Query: 126 LLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQA 185 ++ P+QLSGGQ+QR A+ RA+ QP++ LFDEP S LDA++ +V +I K A Sbjct: 129 QADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEV-LDIMKALATEGI 187 Query: 186 TMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFI 234 TM+ VTH+ A ++DRI+ M G I + G+P D F P + F+ Sbjct: 188 TMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFL 236 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: 206 Number of extensions: 12 Number of successful extensions: 4 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: 241 Length adjustment: 26 Effective length of query: 339 Effective length of database: 215 Effective search space: 72885 Effective search space used: 72885 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: 48 (23.1 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