Align AapJ, 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 GFF3104 Psest_3163 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain
Query= TCDB::Q52812 (341 letters) >FitnessBrowser__psRCH2:GFF3104 Length = 342 Score = 430 bits (1105), Expect = e-125 Identities = 204/336 (60%), Positives = 258/336 (76%), Gaps = 4/336 (1%) Query: 8 AAIGAA-VLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFDVDFCKA 66 A +GAA +L + A + TL V+ KGFVQCG++ GL GF+ DA G + G DVD C+A Sbjct: 9 AVLGAASLLGISGLAQAGATLDAVQKKGFVQCGISDGLPGFSFADAKGKYQGIDVDICRA 68 Query: 67 VASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRPVTYYDG 126 VA+AVFGD +KVKY+P AKERFTALQSGE+DVLSRNTTWT +RD A+G NF VTYYDG Sbjct: 69 VAAAVFGDASKVKYSPLTAKERFTALQSGEVDVLSRNTTWTSSRDAAMGLNFTGVTYYDG 128 Query: 127 QGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLPEVNAAY 186 QGF+V K L V SA EL GA +C+Q+GTTTELNL+DYF+ N +Y P+ ++ E + Sbjct: 129 QGFLVNKELGVSSAKELDGATVCIQAGTTTELNLSDYFRANGHKYTPITYDTSDESAKSL 188 Query: 187 DAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDIVSWTAY 246 ++GRCDV T+DQS LY+ R+ L P ++++LPE+ISKEPLGPAVRQGD++WFDIV WT + Sbjct: 189 ESGRCDVLTSDQSQLYAQRIKLAKPADYVVLPEVISKEPLGPAVRQGDEEWFDIVRWTLF 248 Query: 247 ALINAEEFGITQANVDEM-KNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIKGVGNY 305 A++NAEE G+T ANV+EM K++ NPD+ R LG+E + G DL L DWA ++K VGNY Sbjct: 249 AMLNAEELGVTSANVEEMAKSTKNPDVARLLGAEGE--YGKDLKLPKDWAVQIVKQVGNY 306 Query: 306 GEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341 GEIF+RN+G GS LKI RGLNALWN GG+QYAPPVR Sbjct: 307 GEIFDRNVGAGSELKIERGLNALWNNGGLQYAPPVR 342 Lambda K H 0.316 0.134 0.398 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: 395 Number of extensions: 20 Number of successful extensions: 3 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: 341 Length of database: 342 Length adjustment: 29 Effective length of query: 312 Effective length of database: 313 Effective search space: 97656 Effective search space used: 97656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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