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 SMa0489 SMa0489 ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >FitnessBrowser__Smeli:SMa0489 Length = 255 Score = 345 bits (884), Expect = e-100 Identities = 164/242 (67%), Positives = 204/242 (84%) Query: 15 EVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKI 74 + ++++ + K +G F L+ ++L+V RGE+IV+ GPSGSGKST+IRCINR+EEH G+I Sbjct: 12 DTMIQLIGVGKRFGQFEALKQVSLEVRRGEKIVLCGPSGSGKSTLIRCINRMEEHTSGRI 71 Query: 75 VVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAM 134 ++DG ELT+ K I+ VRREVGMVFQ FNLFPH+TIL+N T+A VRK P+K+A+EVAM Sbjct: 72 IIDGRELTDRTKDINAVRREVGMVFQSFNLFPHMTILKNLTIAQRLVRKTPEKEAKEVAM 131 Query: 135 HFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDT 194 H+LKRVKIPEQA+KYP QLSGGQQQRVAIAR+LCM P+IMLFDEPTSALDPEMI EVLD Sbjct: 132 HYLKRVKIPEQASKYPVQLSGGQQQRVAIARALCMKPQIMLFDEPTSALDPEMISEVLDV 191 Query: 195 MVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQ 254 MV LA +GMTM+CVTHEMGFAR VA+RV+FMD GQ++E+ +P FF NP++ERT LFL Q Sbjct: 192 MVDLARDGMTMICVTHEMGFARSVADRVMFMDGGQLIEEGDPETFFANPRNERTALFLRQ 251 Query: 255 IL 256 IL Sbjct: 252 IL 253 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: 244 Number of extensions: 6 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: 255 Length adjustment: 24 Effective length of query: 233 Effective length of database: 231 Effective search space: 53823 Effective search space used: 53823 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 17 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