Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_013135595.1 ARNIT_RS08945 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_000092245.1:WP_013135595.1 Length = 240 Score = 111 bits (277), Expect = 2e-29 Identities = 82/274 (29%), Positives = 132/274 (48%), Gaps = 49/274 (17%) Query: 9 MSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTM 68 ++++ LL+V L + +G + AI + RG++ ++G NGAGKTT I+G KP Sbjct: 2 VNNEILLEVRDLHVSYGAISAIKGINLTVLRGEVVTILGANGAGKTTTLRTISGLLKPKS 61 Query: 69 GMITFNQKSGKQYLLERLPDFRITKEAR-------VARTFQNIRLFSGLTVLENLLVAQH 121 G I F++ ITK ++ + + R+F LTV ENL++ Sbjct: 62 GNIIFDKND-------------ITKSEAHDIVTLGMSHSPEGRRVFGTLTVEENLMM--- 105 Query: 122 NKLMKASGYTILGLIGVGPYKREAAEAIELARFWLEK--ADLIDRADDPAGDLPYGAQRR 179 YT+ G Y +E + W+ L +R AG L G Q+ Sbjct: 106 ------GAYTLKG------YDKETLD-------WIYDILPRLKERKKQLAGTLSGGEQQM 146 Query: 180 LEIARAMCTGPELLCLDEPAAGLNPRESATLNALLKSIR--AETGTSILLIEHDMSVVME 237 L I RA+ + P+LL LDEP+ GL P + A+ K+I+ A G ++LL+E + ++ Sbjct: 147 LAIGRAIMSKPKLLILDEPSLGLAP---ILIKAIFKAIKEIALNGVTVLLVEQNAKAALK 203 Query: 238 ISDHVVVLEYGQKISDGTPDHVKNDPRVIAAYLG 271 ++D VLE G+ +GT + + N + AYLG Sbjct: 204 LADRAYVLEVGKITHEGTAEELLNSKTIQEAYLG 237 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: 131 Number of extensions: 6 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: 240 Length adjustment: 25 Effective length of query: 267 Effective length of database: 215 Effective search space: 57405 Effective search space used: 57405 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