Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_051302350.1 A3GO_RS0114205 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_000428045.1:WP_051302350.1 Length = 303 Score = 342 bits (878), Expect = 5e-99 Identities = 173/267 (64%), Positives = 212/267 (79%), Gaps = 3/267 (1%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 LL VEHL+M+FGGL+AI+D SF A G+ITA+IGPNGAGKTT+FNCITGFY PT+G +T Sbjct: 20 LLTVEHLTMRFGGLLAIDDVSFAAGEGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 79 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 + G+ +LLER+ FRI + A VARTFQNIRLFS ++VLENL+VAQHN+LMKASG+T+ Sbjct: 80 RAR-GEAFLLERMDGFRIAQRAHVARTFQNIRLFSEMSVLENLIVAQHNELMKASGFTVT 138 Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193 GL G Y+ + EA +LAR+WL++ L AD AG+LPYG QRRLEIARAMC P +L Sbjct: 139 GLFGFRAYRNKEKEATDLARYWLDRVGLTRLADINAGNLPYGDQRRLEIARAMCIKPTIL 198 Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253 CLDEPAAGLNP+ES LN LL I+ E G +LLIEHDMSVVMEISDHV+VL+YG KISD Sbjct: 199 CLDEPAAGLNPKESGGLNNLLNYIKDEHGIGLLLIEHDMSVVMEISDHVIVLDYGSKISD 258 Query: 254 GTPDHVKNDPRVIAAYLGVEDEEVEEV 280 GT +V++DP VI AYLG ++E EE+ Sbjct: 259 GTSLYVRSDPNVIRAYLG--EDETEEL 283 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: 298 Number of extensions: 6 Number of successful extensions: 2 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: 303 Length adjustment: 26 Effective length of query: 266 Effective length of database: 277 Effective search space: 73682 Effective search space used: 73682 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: 48 (23.1 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