Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_061532832.1 CAter10_RS06905 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_001584165.1:WP_061532832.1 Length = 254 Score = 200 bits (508), Expect = 3e-56 Identities = 114/263 (43%), Positives = 163/263 (61%), Gaps = 10/263 (3%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 +L+++++S FGGL + D +F +G I LIGPNGAGKTTVFN ITG + + G I F Sbjct: 2 MLQLKNISKNFGGLQVLQDVNFNVPQGGIFGLIGPNGAGKTTVFNLITGLLRASGGAIEF 61 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 + + + ++ +IT E +ARTFQNIR+F +T+LEN++V H+ + G + Sbjct: 62 DGQD-----IGKVAPHKIT-ERGIARTFQNIRVFKEMTLLENVVVGMHDHMDYGFGSLLF 115 Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193 L G Y++ A+A E A L L +A A L YG QR+LE ARA+ T P+LL Sbjct: 116 NL---GGYRKVEAQARERALELLSWVRLDHKAHTLADSLSYGEQRKLEFARALATKPKLL 172 Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253 LDEP AG+NP E L A + +I+ + G SI +IEHDM VM + D + VL +G+ I++ Sbjct: 173 LLDEPVAGMNPAEKTELMAEILNIK-QRGFSIFMIEHDMRFVMGLCDRIAVLNFGRIIAE 231 Query: 254 GTPDHVKNDPRVIAAYLGVEDEE 276 G+PD +KN+ VI AYLG E+ E Sbjct: 232 GSPDQIKNNQEVIEAYLGKEEAE 254 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: 198 Number of extensions: 8 Number of successful extensions: 4 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: 254 Length adjustment: 25 Effective length of query: 267 Effective length of database: 229 Effective search space: 61143 Effective search space used: 61143 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: 47 (22.7 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