Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Ga0059261_0341 Ga0059261_0341 ABC-type antimicrobial peptide transport system, ATPase component
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Korea:Ga0059261_0341 Length = 224 Score = 108 bits (271), Expect = 1e-28 Identities = 73/201 (36%), Positives = 105/201 (52%), Gaps = 11/201 (5%) Query: 19 VLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNV 78 VL +DL +G GE V LLGPSG GKST+L+ + LE G++RI G V L + R V Sbjct: 24 VLRGIDLTVGQGEIVALLGPSGSGKSTLLQAVGLLEGGFEGSIRISGVEVGKLESHARTV 83 Query: 79 A------MVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAAL--LNLEALLER 130 V+Q + L P + +N+ L +L + A D R R L L L A L Sbjct: 84 TRRDKLGFVYQFHHLLPDFNALENVE--LPQLIQNATLADARARSEGLLTALGLGARLTH 141 Query: 131 KPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVY 190 +P +SGG+QQR A+ARA+ P++ L DEP NLD + + RL + + Sbjct: 142 RPSQLSGGEQQRVAVARALANRPALVLADEPTGNLDEHTADIVLAEFLRLVRGEGAAALI 201 Query: 191 VTHDQLEAMTLADRVILMQDG 211 TH++ A + DRV+ + +G Sbjct: 202 ATHNERLAAKM-DRVVRLHEG 221 Lambda K H 0.321 0.137 0.403 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: 208 Number of extensions: 6 Number of successful extensions: 2 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: 406 Length of database: 224 Length adjustment: 27 Effective length of query: 379 Effective length of database: 197 Effective search space: 74663 Effective search space used: 74663 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 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