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 Ac3H11_4899 ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4899 Length = 264 Score = 244 bits (623), Expect = 1e-69 Identities = 132/253 (52%), Positives = 172/253 (67%), Gaps = 1/253 (0%) Query: 4 APAKKLTVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCI 63 APA V V+I + K YG VL+ I+LKV RGE I I G SGSGKST++RC+ Sbjct: 10 APAHDGIVVGEPPIVDITALRKSYGSNEVLKGIDLKVQRGEVIAIIGKSGSGKSTLLRCV 69 Query: 64 NRLEEHQKGKIVVDGTELTNDLKK-IDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVR 122 N LEE Q+G + V+G +L +D + E+R++VGM+FQ FNLFPHL++ N LAP V+ Sbjct: 70 NGLEEFQEGALSVNGKKLLHDSPTAMRELRQQVGMIFQSFNLFPHLSVGRNIMLAPTLVK 129 Query: 123 KMPKKQAEEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSA 182 K AE A L+RV + E+ + P QLSGGQQQRVAIAR+L M P+++L DE TSA Sbjct: 130 ARDAKTAETQARKLLERVGLAEKFDAMPDQLSGGQQQRVAIARALAMEPQVLLCDEITSA 189 Query: 183 LDPEMIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDN 242 LDPE++ EVL + LA+EGMT++ VTHEM FAR+V +RVIFM QG++ EQ PAA F N Sbjct: 190 LDPELVGEVLRVVESLAQEGMTLMMVTHEMAFARKVGDRVIFMHQGRVHEQGTPAALFGN 249 Query: 243 PQHERTKLFLSQI 255 PQ + FLS + Sbjct: 250 PQTPELQQFLSSL 262 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: 203 Number of extensions: 5 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: 264 Length adjustment: 25 Effective length of query: 232 Effective length of database: 239 Effective search space: 55448 Effective search space used: 55448 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