Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_269208425.1 MMARC5_RS07475 amino acid ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_000016125.1:WP_269208425.1 Length = 240 Score = 105 bits (261), Expect = 1e-27 Identities = 70/213 (32%), Positives = 112/213 (52%), Gaps = 4/213 (1%) Query: 27 LAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFEGRDITRMPTH-EIAR 85 L GVD+ V KGE++ ++G +G+GKSTL+ I G + G + FEG DIT + R Sbjct: 14 LKGVDLKVAKGEVLVIVGPSGSGKSTLLRCINGLEKITEGHMYFEGDDITDKKVNINKIR 73 Query: 86 LRIAQSPEGRRIFPRMTVLENLQMGAG--LDNLKHFAEDVEKIFTLFPRLKERHAQRGGT 143 +I + +FP +TVL+N+ L K AE + L+ + Q Sbjct: 74 QKIGMVFQQFNLFPHLTVLDNITFAPRKVLKVSKKEAETLAMELLKKVGLEGKENQYPIQ 133 Query: 144 LSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLNEAEGLTVFLVEQN 203 LSGG+QQ ++I RAL +P +L DEP+ L P +VK + + +++L EG+T+ +V Sbjct: 134 LSGGQQQRVAIARALAMKPDAMLFDEPTSALDPELVKEVLDVMKQL-AYEGMTMVVVTHE 192 Query: 204 AFAALRLSHRAYVMVNGKVTMSGSGKELLANPE 236 A + R + NG++ G E+ +NP+ Sbjct: 193 MGFAKEVGDRLIFIDNGQILEDGDPAEIFSNPK 225 Lambda K H 0.320 0.137 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: 8 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: 247 Length of database: 240 Length adjustment: 23 Effective length of query: 224 Effective length of database: 217 Effective search space: 48608 Effective search space used: 48608 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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