Align ATPase (characterized, see rationale)
to candidate Dsui_2877 Dsui_2877 ABC-type antimicrobial peptide transport system, ATPase component
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__PS:Dsui_2877 Length = 248 Score = 151 bits (381), Expect = 1e-41 Identities = 95/234 (40%), Positives = 135/234 (57%), Gaps = 8/234 (3%) Query: 12 TAIASAPETMIYAEGVEKWYGNQ---FQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTL 68 TA A A +I G++K Y F L GVSL + GE V +MGPSGSGKSTF+ L Sbjct: 5 TASADAA-AVIEVAGLDKAYDTPMGPFPVLKGVSLAIHAGEFVAIMGPSGSGKSTFMNIL 63 Query: 69 NALESHQRGEIWIEGHRLSH-DRRDIATIRQE-VGMVFQQFNLFPHLTVLQNLMLAPVQV 126 L+ G+ ++G +S D+ A +R +G VFQ FNL P +++ N+ L P+ Sbjct: 64 GCLDRPSGGDYILDGKHVSALDKDQTALLRNRTIGFVFQGFNLLPRMSLEDNVAL-PLVY 122 Query: 127 RRWPVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTS 186 + AR+LL +V + + A P ++SGGQQQRVAIARAL +PR++L DEPT Sbjct: 123 CGVDKEERRQRARELLAKVGLGQYAKSLPNRISGGQQQRVAIARALVNRPRLILADEPTG 182 Query: 187 ALDPEMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAP 240 LD E++ + +L EG+T+++ THE A+ A R V DG+IV +AP Sbjct: 183 NLDSHTSEEIMALFEELNREGITIVLVTHEPDIAQH-AKRQVRFLDGRIVHDAP 235 Lambda K H 0.321 0.134 0.387 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: 166 Number of extensions: 10 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: 261 Length of database: 248 Length adjustment: 24 Effective length of query: 237 Effective length of database: 224 Effective search space: 53088 Effective search space used: 53088 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 (21.9 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