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_004144835.1 Mesci_5725 ABC transporter
Query= TCDB::Q52815 (257 letters) >NCBI__GCF_000185905.1:YP_004144835.1 Length = 246 Score = 349 bits (895), Expect = e-101 Identities = 163/243 (67%), Positives = 200/243 (82%) Query: 14 TEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGK 73 ++ +E N++KWYG F L D+NL V +GERIVI GPSGSGKST+IRC NRLE HQ+G+ Sbjct: 2 SDTVIEAKNVSKWYGTFRALTDVNLTVRKGERIVICGPSGSGKSTLIRCFNRLEAHQEGE 61 Query: 74 IVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVA 133 I V+G L N ++ + EVR VGMVFQHFNLFPH+T+L NC AP+W++ M + +A+++A Sbjct: 62 ITVNGIRLHNKMRDLAEVRTNVGMVFQHFNLFPHMTVLMNCMAAPMWIKGMSEAEAKKIA 121 Query: 134 MHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLD 193 + FL+RV+IPEQANK+PGQLSGGQQQRVAIARSLCM P +MLFDEPTS+LDPEM+ EVL+ Sbjct: 122 LKFLERVRIPEQANKFPGQLSGGQQQRVAIARSLCMEPAVMLFDEPTSSLDPEMVAEVLE 181 Query: 194 TMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLS 253 TM LA EGMTM+CVTHEMGFAR VA+RVIFMD G+IVE+ +P FF PQHERTKLFL Sbjct: 182 TMTSLAREGMTMVCVTHEMGFARSVADRVIFMDAGRIVEEGKPHDFFTKPQHERTKLFLH 241 Query: 254 QIL 256 QIL Sbjct: 242 QIL 244 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: 8 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: 246 Length adjustment: 24 Effective length of query: 233 Effective length of database: 222 Effective search space: 51726 Effective search space used: 51726 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 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