Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease
Query= uniprot:A0A1I1Y8J0 (492 letters) >NCBI__GCF_002117405.1:WP_085770386.1 Length = 488 Score = 364 bits (934), Expect = e-105 Identities = 205/488 (42%), Positives = 288/488 (59%), Gaps = 26/488 (5%) Query: 2 LKNLFATTQISPASADLPGGGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAE 61 L LF I A+ GA L+RAL LV +G+G +IG GIFV+TG AA Sbjct: 3 LVELFRAKSIESLQAEALERGA-----LRRALGLWQLVGIGLGGLIGVGIFVLTGVVAAT 57 Query: 62 HAGPAIVLSFVFAGIACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLE 121 AGP + LSF+ AG+A AALCYAEFA+MLPV+GSAY+Y+YA LGE AW +GW L+LE Sbjct: 58 QAGPGVALSFLIAGVASGAAALCYAEFASMLPVAGSAYTYAYAVLGELPAWIIGWDLLLE 117 Query: 122 YLFTVATVAAGWSGYFNKLLALISGWIGHDVSLPQTLAAAPFTVVDGHIQATGMFINLPA 181 Y VA V+ GWSGY LLAL V+ P+ A AP T DGHI +F L A Sbjct: 118 YALVVAVVSIGWSGYLRALLALFG------VAPPEWAAGAPGT-GDGHI--LDLFAMLGA 168 Query: 182 VAIIAAITGLCYVGITQSAFVNSIIVAIKVTVILLFIAFATKYINPDNWHPFIPASEGAS 241 + +T + + A N+ +V +K+ +++ I A +INP NW PF+P Sbjct: 169 FGVALLLT----LRVEWGARFNTAMVLLKIAAVIVVILAAAPHINPANWRPFMP------ 218 Query: 242 KYGWAGVGRAAAIVFFSYIGFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGIL 301 +G+ GV AA+VFF+ G+D ++TA EA PQRD+P ++ SL++ LYI+++ L Sbjct: 219 -FGFGGVVEGAAVVFFAVFGYDTLTTAGEEALEPQRDLPRAVLLSLVVSLTLYILMSLAL 277 Query: 302 TGIADFRLLGTPEPVSTALDNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMAR 361 TGIA + L PV++A + W ++V AV G+ SVML L+G RI+++M+R Sbjct: 278 TGIARYDTLDNAAPVASAFAAL-GMGWATLVVSAAAVVGILSVMLAFLLGCARIWFAMSR 336 Query: 362 DGLIPAVFGRIHQKFRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGV 421 DGL+PA F R H +F TP+ T++ G L A + F I + E+V +GTL AF +C+ V Sbjct: 337 DGLLPAWFARPHPQFATPYRPTLIAGGLCALVSAFFPIREVAELVNIGTLSAFVVICLAV 396 Query: 422 LVLRYTRPELPRAFRVPVPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYG 481 + LR+TRP++PR FR P+ + +G + L + W + W+ IG A+YFLYG Sbjct: 397 IALRHTRPDVPRGFRAPLSPYLPLIGVGFSLWLLSKLPAIAWERFVVWLIIGLAVYFLYG 456 Query: 482 YSHSKLRK 489 HS+L K Sbjct: 457 RRHSRLAK 464 Lambda K H 0.328 0.141 0.441 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: 715 Number of extensions: 45 Number of successful extensions: 5 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: 492 Length of database: 488 Length adjustment: 34 Effective length of query: 458 Effective length of database: 454 Effective search space: 207932 Effective search space used: 207932 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: 52 (24.6 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