Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Ga0059261_1321 Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >FitnessBrowser__Korea:Ga0059261_1321 Length = 238 Score = 128 bits (322), Expect = 1e-34 Identities = 80/221 (36%), Positives = 115/221 (52%), Gaps = 11/221 (4%) Query: 4 LQLRGIEKFFGE----HRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGS 59 ++LR I K FGE +A+KG+DL I + +F+ +GPSG GKST + ++ L+ G Sbjct: 8 IRLRNITKVFGEGATAFQALKGVDLDIAERDFVAVMGPSGSGKSTTMNILGCLDVPTSGE 67 Query: 60 LMLDGRDITDQPSSKRDLA------MVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEK 113 + G I +R L VFQ + L + EN+ L DK+V E Sbjct: 68 FLFKGVYIETLDRDQRALVRRKYLGFVFQGFNLLSRTNALENVELPLLYRGEDKKVRHEL 127 Query: 114 VQNAARILNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTR 173 A + L + TP ELSGGQ QRVAI RAIV +P V L DEP NLD+A + Sbjct: 128 GMAALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPAVLLADEPTGNLDSARSVEIM 187 Query: 174 VEIAKLHRDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQ 214 + L++D G T + VTH+ + A +V +DG++E+ Sbjct: 188 ELLTSLNKDSGITVLMVTHEP-DMAAFARTIVHFKDGLVER 227 Lambda K H 0.320 0.137 0.388 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: 181 Number of extensions: 9 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: 350 Length of database: 238 Length adjustment: 26 Effective length of query: 324 Effective length of database: 212 Effective search space: 68688 Effective search space used: 68688 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: 47 (22.7 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