Align AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate WP_085636165.1 MGEO_RS07775 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_002115805.1:WP_085636165.1 Length = 263 Score = 387 bits (994), Expect = e-112 Identities = 187/242 (77%), Positives = 218/242 (90%) Query: 15 EVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKI 74 EV +EI M+K+YG F VL DI+L+V RGERIVI GPSGSGKST+IRC+NRLEEHQ+G+I Sbjct: 20 EVVIEIEKMSKFYGAFQVLHDIDLQVRRGERIVICGPSGSGKSTLIRCLNRLEEHQEGRI 79 Query: 75 VVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAM 134 V+DG ELT+DLK ID+VR E+GM FQHFNLFPHLTILENCTLAP+ R+ P+++AE AM Sbjct: 80 VIDGVELTSDLKNIDKVRSEIGMCFQHFNLFPHLTILENCTLAPMLARQTPREEAEATAM 139 Query: 135 HFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDT 194 FL++VKIP+QA KYPGQLSGGQQQRVAIAR+LCM P+IMLFDEPTSALDPEMIKEVLDT Sbjct: 140 RFLEKVKIPDQAGKYPGQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMIKEVLDT 199 Query: 195 MVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQ 254 MV LAEEGMTMLCVTHEMGFA+ VANRVIFMDQG+IVE+N P+AFF+NPQ+ERT+ FLSQ Sbjct: 200 MVELAEEGMTMLCVTHEMGFAQAVANRVIFMDQGRIVEENGPSAFFNNPQNERTQAFLSQ 259 Query: 255 IL 256 I+ Sbjct: 260 II 261 Lambda K H 0.321 0.135 0.394 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: 279 Number of extensions: 4 Number of successful extensions: 1 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: 257 Length of database: 263 Length adjustment: 24 Effective length of query: 233 Effective length of database: 239 Effective search space: 55687 Effective search space used: 55687 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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