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 Pf1N1B4_917 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
Query= TCDB::Q52812 (341 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_917 Length = 343 Score = 400 bits (1028), Expect = e-116 Identities = 196/343 (57%), Positives = 248/343 (72%), Gaps = 4/343 (1%) Query: 1 MKNKLLSAAIGAAVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFD 60 M L+ AAVL V A + TL V+ KGFVQCGV+ GL GF+ PD++G G D Sbjct: 3 MLKSTLAIVTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGID 62 Query: 61 VDFCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRP 120 DFC+AVA+AVFGD TKVK++ NAKERFTALQSGEIDVLSRN+T T +RD +G F Sbjct: 63 ADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDVLSRNSTMTSSRDAGMGLKFPG 122 Query: 121 -VTYYDGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENL 179 +TYYDG GF+ L VKSA EL GA IC+Q+GTTTELN++DYF+ N L+Y P+ F+ Sbjct: 123 FITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTS 182 Query: 180 PEVNAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFD 239 E + ++GRCDV T+D+S L++ R L +P ++++LPE ISKEPLGP VR GDD+W Sbjct: 183 DESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLA 242 Query: 240 IVSWTAYALINAEEFGITQANVD-EMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANV 298 IV WT YAL+NAEE G+T NV+ E K++ NPD+ R LG+ D + G DL L DW + Sbjct: 243 IVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGA--DGEYGKDLKLPKDWVVKI 300 Query: 299 IKGVGNYGEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341 +K VGNYGE+FERN+G+ +PL+I RGLNALWN GGIQYAPPVR Sbjct: 301 VKQVGNYGEMFERNLGKDTPLQIDRGLNALWNAGGIQYAPPVR 343 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: 373 Number of extensions: 19 Number of successful extensions: 4 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: 343 Length adjustment: 29 Effective length of query: 312 Effective length of database: 314 Effective search space: 97968 Effective search space used: 97968 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 Apr 09 2024. 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