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_008504347.1 BIBO1_RS07180 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_000182725.1:WP_008504347.1 Length = 269 Score = 471 bits (1212), Expect = e-138 Identities = 228/255 (89%), Positives = 242/255 (94%) Query: 3 EAPAKKLTVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRC 62 E K+ VS TEVA+EI NM+KWYG+FHVLRDINLKVMRGERIV+AGPSGSGKSTMIRC Sbjct: 15 EVDRSKMQVSKTEVAIEITNMHKWYGEFHVLRDINLKVMRGERIVVAGPSGSGKSTMIRC 74 Query: 63 INRLEEHQKGKIVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVR 122 INRLEEHQKG+IVVDG ELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVR Sbjct: 75 INRLEEHQKGEIVVDGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVR 134 Query: 123 KMPKKQAEEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSA 182 KMPKKQAEE+AMH+L+RVKIPEQANKYPGQLSGGQQQRVAIAR+LCMNPK+MLFDEPTSA Sbjct: 135 KMPKKQAEEIAMHYLERVKIPEQANKYPGQLSGGQQQRVAIARALCMNPKVMLFDEPTSA 194 Query: 183 LDPEMIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDN 242 LDPEM+KEVLDTMV LA EGMTM+CVTHEMGFARQVANRVIFMDQGQIVEQN P FFDN Sbjct: 195 LDPEMVKEVLDTMVSLAAEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPDEFFDN 254 Query: 243 PQHERTKLFLSQILH 257 PQHERT+LFLSQILH Sbjct: 255 PQHERTRLFLSQILH 269 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: 335 Number of extensions: 7 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: 269 Length adjustment: 25 Effective length of query: 232 Effective length of database: 244 Effective search space: 56608 Effective search space used: 56608 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