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 206675 DVU1236 amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q52815 (257 letters) >MicrobesOnline__882:206675 Length = 247 Score = 302 bits (773), Expect = 5e-87 Identities = 148/245 (60%), Positives = 191/245 (77%) Query: 12 SATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQK 71 +A E + I N+ K++G+ L D++L V GE++VI GPSGSGKST++R INRLE K Sbjct: 3 AANEPIISIRNVWKFFGELTALHDVSLDVQAGEKVVIIGPSGSGKSTLLRSINRLENVDK 62 Query: 72 GKIVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEE 131 G I+VDG ++ + I+ +R+++GMVFQ FNLFPH T+L+N T+AP+ +RK+P+ +AE Sbjct: 63 GSIIVDGKDIRAEDSDINVIRQDLGMVFQSFNLFPHKTVLQNLTMAPMRLRKVPRDEAES 122 Query: 132 VAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEV 191 A+ LK+V I ++AN YP LSGGQQQRVAIAR+L MNPKIMLFDEPTSALDPEMI EV Sbjct: 123 RALDLLKKVGISDKANVYPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMIGEV 182 Query: 192 LDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLF 251 LD MV LA+EGMTM+CVTHEMGFAR+VA+R+IFMD GQI+EQ P FF+ P+H R + F Sbjct: 183 LDVMVTLAKEGMTMVCVTHEMGFAREVADRIIFMDHGQILEQGTPQHFFEAPEHPRLQKF 242 Query: 252 LSQIL 256 L QIL Sbjct: 243 LQQIL 247 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: 217 Number of extensions: 5 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: 247 Length adjustment: 24 Effective length of query: 233 Effective length of database: 223 Effective search space: 51959 Effective search space used: 51959 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: 46 (22.3 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