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 YP_004141764.1 Mesci_2578 ABC transporter
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_000185905.1:YP_004141764.1 Length = 252 Score = 349 bits (896), Expect = e-101 Identities = 168/247 (68%), Positives = 205/247 (82%) Query: 10 TVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEH 69 T S E A+ I N++K+YG F LR INL V RGE+IV+ GPSGSGKSTMIRCINRLE+H Sbjct: 4 TNSTGEPALRIENLDKYYGTFQALRGINLSVQRGEKIVVCGPSGSGKSTMIRCINRLEQH 63 Query: 70 QKGKIVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQA 129 G+I V GTEL +D+ IDE+RREVGMVFQHFNLFPH+T+LENC ++P+ VRK P+ QA Sbjct: 64 NGGRIAVLGTELNDDVGNIDEIRREVGMVFQHFNLFPHMTVLENCMISPMIVRKQPRAQA 123 Query: 130 EEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIK 189 E A H+L++V+IPEQA KYP QLSGGQQQRVAIAR+LCM P+IMLFDEPTSALDPEM+ Sbjct: 124 EATARHYLEKVRIPEQAMKYPSQLSGGQQQRVAIARALCMQPQIMLFDEPTSALDPEMVS 183 Query: 190 EVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTK 249 EVLD MV LA EGMTM+CVTHEMGFAR+VA+RV+FMD G+I+E+ P FF + ++ERT+ Sbjct: 184 EVLDVMVTLASEGMTMICVTHEMGFARRVADRVLFMDGGEILEEAPPDEFFTSSRNERTR 243 Query: 250 LFLSQIL 256 F+SQ+L Sbjct: 244 QFVSQVL 250 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: 234 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: 252 Length adjustment: 24 Effective length of query: 233 Effective length of database: 228 Effective search space: 53124 Effective search space used: 53124 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