Align ATPase (characterized, see rationale)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__Pedo557:CA265_RS07485 Length = 252 Score = 144 bits (364), Expect = 1e-39 Identities = 86/201 (42%), Positives = 120/201 (59%), Gaps = 4/201 (1%) Query: 37 ALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRLSHDRRD-IAT 95 AL VSL + +GE V +MGPSGSGKST + L L++ G + G +SH D +A Sbjct: 24 ALKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDALAE 83 Query: 96 IR-QEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKY 154 +R QE+G VFQ FNL P T L N+ L P+ +A A + LE V + + D Sbjct: 84 VRNQEIGFVFQTFNLLPRSTSLDNVAL-PLIYAGTSKKDRDARAARALENVGLGNRMDHK 142 Query: 155 PGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLASEGMTMLVAT 214 P +LSGGQ+QRVA+ARAL P I+L DEPT LD + E++ ++ ++ S+G T+++ T Sbjct: 143 PNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIHSKGNTIILVT 202 Query: 215 HEVGFAREVADRVVLMADGQI 235 HE A+ A R+V M DG I Sbjct: 203 HEEDIAQH-AHRIVRMRDGLI 222 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: 128 Number of extensions: 5 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: 252 Length adjustment: 24 Effective length of query: 237 Effective length of database: 228 Effective search space: 54036 Effective search space used: 54036 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