Align ATPase (characterized, see rationale)
to candidate 6937298 Sama_1468 putative macrolide efflux ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__SB2B:6937298 Length = 230 Score = 140 bits (354), Expect = 2e-38 Identities = 84/212 (39%), Positives = 124/212 (58%), Gaps = 5/212 (2%) Query: 34 QFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRLSHDRRDI 93 + QAL GV + +++ E V +MGPSGSGKST + + L+ G + G + D Sbjct: 17 EVQALRGVDIHIRQNEFVAIMGPSGSGKSTLMNIIGCLDRPTSGNYLLNGSAVGGLSDDA 76 Query: 94 --ATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQA 151 A +E+G VFQ F+L P L+ L N++L P++ P + A +LLERV + ++ Sbjct: 77 LSAVRNREIGFVFQSFHLLPRLSALDNVLL-PLRFSETPRGDRQH-AIELLERVGLGQRL 134 Query: 152 DKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLASEGMTML 211 D P QLSGGQ+QRVAIARAL +P +LL DEPT ALD + E++ + +L G T++ Sbjct: 135 DHRPNQLSGGQRQRVAIARALVNRPTLLLADEPTGALDSKTSVEIMALFDELHLSGQTIV 194 Query: 212 VATHEVGFAREVADRVVLMADGQIVEEAPPDR 243 + THE A E A R++ M DG + ++ R Sbjct: 195 LVTHEEEVA-ECAGRIIRMRDGVVQQDKQKPR 225 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: 139 Number of extensions: 10 Number of successful extensions: 3 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: 230 Length adjustment: 24 Effective length of query: 237 Effective length of database: 206 Effective search space: 48822 Effective search space used: 48822 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: 46 (22.3 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