Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_047214486.1 PATSB16_RS12750 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_001931675.1:WP_047214486.1 Length = 274 Score = 199 bits (505), Expect = 7e-56 Identities = 117/262 (44%), Positives = 161/262 (61%), Gaps = 10/262 (3%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 +L + +S FGGL + D + E +G I LIGPNGAGKTTVFN ITG P+ G ITF Sbjct: 1 MLTLSSVSKSFGGLHVLQDVNIEVPQGTIFGLIGPNGAGKTTVFNLITGLLAPSGGDITF 60 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 + S LL P RIT+ +ARTFQNIR+F +++L+N++V H L +L Sbjct: 61 DGAS----LLGHKP-HRITQRG-IARTFQNIRIFKEMSLLDNVVVGMHRHLDYGPAGLLL 114 Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193 L G Y+R A E A L L +A + A +L YG QR+LE+ARA+ T P+LL Sbjct: 115 SLPG---YRRHEKRARERAHELLSWVRLDHKAHETADNLSYGDQRKLELARALATEPKLL 171 Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253 LDEP AG+N E L +++IRA G +I +IEHDM VM + + + VL +G+ I++ Sbjct: 172 LLDEPVAGMNTGEKVDLMGEIENIRAR-GYTIFMIEHDMRFVMGLCERIAVLNFGRIIAE 230 Query: 254 GTPDHVKNDPRVIAAYLGVEDE 275 G PD +KN+P+VI AYLG +D+ Sbjct: 231 GKPDEIKNNPQVIEAYLGSDDD 252 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: 257 Number of extensions: 15 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: 274 Length adjustment: 26 Effective length of query: 266 Effective length of database: 248 Effective search space: 65968 Effective search space used: 65968 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