Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_067913242.1 AQZ52_RS15945 ATP-binding cassette domain-containing protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_001519075.1:WP_067913242.1 Length = 208 Score = 92.4 bits (228), Expect = 7e-24 Identities = 70/210 (33%), Positives = 99/210 (47%), Gaps = 25/210 (11%) Query: 37 AKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITFNQKSGKQYLLERLPDFRITKEAR 96 A G ITAL+GP+GAGK++V + G +P G I G L + L + EAR Sbjct: 21 ASAGGITALVGPSGAGKSSVLEALAGLLRPEAGRIAV----GGTVLFDSLARVNLPPEAR 76 Query: 97 VART-FQNIRLFSGLTVLENLLVAQHNKLMKASGYTILGLIGVGPYKREAAEAIELARFW 155 FQ++RLF VL NLL Q + P +R E+A F Sbjct: 77 ACGVMFQDLRLFPHRRVLGNLLYGQR----------------LAPPERRFLSLEEVADF- 119 Query: 156 LEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELLCLDEPAAGLNPRESATLNALLK 215 L+ A L+ R L G +R+ I RA+ +GP L +DEP L+ + A+++ Sbjct: 120 LDIAPLLGRRPRT---LSGGEAQRVAIGRALLSGPRFLLMDEPLTALDDARREAIIAVIE 176 Query: 216 SIRAETGTSILLIEHDMSVVMEISDHVVVL 245 IR E ILL+ HD + V ++D VV L Sbjct: 177 RIRDELALPILLVSHDRADVARLADTVVEL 206 Lambda K H 0.318 0.136 0.386 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: 156 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: 292 Length of database: 208 Length adjustment: 24 Effective length of query: 268 Effective length of database: 184 Effective search space: 49312 Effective search space used: 49312 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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