Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 236 bits (603), Expect = 6e-67 Identities = 126/290 (43%), Positives = 183/290 (63%), Gaps = 17/290 (5%) Query: 4 VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63 +TL + KR+ + EV+ +L ++D EF ++GPSGCGK+T LR+IAG E+ + G I + Sbjct: 7 LTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLN 66 Query: 64 GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDL 123 G + +P R + VFQSYAL+PH+TV +N+ F LK+AG ++I RVA+A AI+ L Sbjct: 67 GDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRL 126 Query: 124 AHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARM 183 + R+P QLSGGQ+QRVA+ RA+V +P + L DE LS LD KLR Q++ E+K+L ++ Sbjct: 127 SEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQL 186 Query: 184 QATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEE 243 T +YVTHDQ EA+++SDRI++M +G +QVGTP +++ P FVA FIG E Sbjct: 187 GITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIG-------E 239 Query: 244 AVLTDGKLAFASGATLPLPPRFRSLVRE---------GQKVTFGLRPDDV 284 + DG++ A G +VRE G KV LRP+D+ Sbjct: 240 INVFDGEIVQALG-EYQYEASINGVVREIRCDHRFAVGDKVHVMLRPEDL 288 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: 332 Number of extensions: 9 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: 369 Length adjustment: 30 Effective length of query: 335 Effective length of database: 339 Effective search space: 113565 Effective search space used: 113565 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