Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_058932742.1 AU252_RS04325 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8YXD0 (288 letters) >NCBI__GCF_001484605.1:WP_058932742.1 Length = 481 Score = 182 bits (461), Expect = 2e-50 Identities = 106/280 (37%), Positives = 165/280 (58%), Gaps = 2/280 (0%) Query: 6 IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGVNIWLSM 65 + +V G++ G ++ALA+VGL+L +G L+NFAHG+ +TLGA L F N G+ WL++ Sbjct: 194 VNRLVAGLSFGLLLALASVGLSLIFGTTGLTNFAHGEMVTLGAVLVFAFNAIGLPFWLAL 253 Query: 66 IVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNYNL 125 I++++G + + LW +R ++I+SIGLAL +R I +GG Q Sbjct: 254 ILSLLGGGLFGYIQDAGLWKPLRRRGTGLVPMMIVSIGLALAVRYVIQFYFGGATQQLPF 313 Query: 126 PITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKVSGID 185 + + + + + N L L ++ + I L +L T++GKA RAVAD+ LA SGID Sbjct: 314 AQSAEIQLGPISISPNNLWSLIVSAVVIALLGIVLLKTRLGKATRAVADNPALAAASGID 373 Query: 186 VEQVIFWTWLIAGTVTSLGGSMYGLI-TAVRPNMGWFLILPLFASVILGGIGNPYGAIAA 244 V+ VI W+ G + SLGG ++ V +MG ++L +FA V LGG+G +GA+ Sbjct: 374 VDSVIRIVWVTGGMLASLGGILWAYYRPGVTFDMGSQILLLIFAGVTLGGLGTVFGALIG 433 Query: 245 AFIIGIVQEVSTPF-LGSQYKQGVALLIMILVLLIRPKGL 283 + I+GI E++T F L + K AL IMI+VLL RP+G+ Sbjct: 434 SIIVGIFVELTTVFGLAADLKYVGALFIMIVVLLFRPQGI 473 Lambda K H 0.328 0.144 0.426 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: 387 Number of extensions: 23 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: 288 Length of database: 481 Length adjustment: 30 Effective length of query: 258 Effective length of database: 451 Effective search space: 116358 Effective search space used: 116358 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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