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 N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= TCDB::Q52815 (257 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 163 bits (412), Expect = 5e-45 Identities = 96/245 (39%), Positives = 140/245 (57%), Gaps = 6/245 (2%) Query: 18 VEIVNMNKWYG----DFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGK 73 + V+++K Y D L+ +L + GE I G SG+GKST+IR IN LE G Sbjct: 2 IRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGS 61 Query: 74 IVVDGTELTN-DLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEV 132 I++DGTE+T + RR +GM+FQHFNL T+ +N + + + Sbjct: 62 ILIDGTEMTALGDAALRAQRRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKAR 121 Query: 133 AMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVL 192 L+RV + A+KYP QLSGGQ+QRV IAR+L P I+L DE TSALDP+ VL Sbjct: 122 VDELLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVL 181 Query: 193 DTMVGLAEE-GMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLF 251 + + + E +T++ +THEM R+V +RV +D G+IVE A F +P+H T+ F Sbjct: 182 ELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRF 241 Query: 252 LSQIL 256 +++ L Sbjct: 242 VNEAL 246 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: 202 Number of extensions: 10 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: 257 Length of database: 336 Length adjustment: 26 Effective length of query: 231 Effective length of database: 310 Effective search space: 71610 Effective search space used: 71610 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: 48 (23.1 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