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_043531246.1 JH15_RS13610 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_000759345.1:WP_043531246.1 Length = 257 Score = 293 bits (749), Expect = 3e-84 Identities = 151/242 (62%), Positives = 184/242 (76%), Gaps = 3/242 (1%) Query: 18 VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77 V + +NK +GD HVL+DI+L++ GE +VI G SGSGKST+IRC+N LEE Q G I VD Sbjct: 14 VRMDKVNKHFGDLHVLKDIDLEIAPGEVVVIIGASGSGKSTLIRCVNGLEEFQYGHIEVD 73 Query: 78 GTELT---NDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAM 134 G EL K + +R EVGMVFQ FNLFPHL++L+N TLAPI VR P++QA A Sbjct: 74 GNELLPNGKSAKALQTIRTEVGMVFQQFNLFPHLSVLDNVTLAPIKVRGTPRQQAVANAR 133 Query: 135 HFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDT 194 L+RV I +QA+K P QLSGGQQQRVA+AR+L M P++MLFDEPTSALDPEMI EVLD Sbjct: 134 RLLERVGIADQADKSPTQLSGGQQQRVALARALTMEPRLMLFDEPTSALDPEMIGEVLDA 193 Query: 195 MVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQ 254 M LA +GMTM+ VTHEMGFAR+VA+RVI++ GQIVEQ P FDNPQHERT+ FLS+ Sbjct: 194 MRELARDGMTMMIVTHEMGFAREVADRVIYIHGGQIVEQGPPGVVFDNPQHERTQSFLSR 253 Query: 255 IL 256 +L Sbjct: 254 VL 255 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: 230 Number of extensions: 7 Number of successful extensions: 2 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: 257 Length adjustment: 24 Effective length of query: 233 Effective length of database: 233 Effective search space: 54289 Effective search space used: 54289 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