Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate N515DRAFT_0606 N515DRAFT_0606 basic amino acid/polyamine antiporter, APA family
Query= uniprot:A0A1I1Y8J0 (492 letters) >FitnessBrowser__Dyella79:N515DRAFT_0606 Length = 477 Score = 367 bits (943), Expect = e-106 Identities = 197/464 (42%), Positives = 275/464 (59%), Gaps = 18/464 (3%) Query: 30 KRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCYAEFA 89 +R L L +GIG IIG G+FV+ GQ AA +AGPA+ +SF+ AGIA A AALCYAEFA Sbjct: 27 RRVLGLWQLTAIGIGGIIGVGVFVLAGQQAALNAGPAVAISFLIAGIASAAAALCYAEFA 86 Query: 90 AMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALISGWIG 149 ++PV+GSAY+Y YA LGE AW +GW L+LEY VA VA GWSGY LA I Sbjct: 87 GLIPVTGSAYTYGYAVLGELAAWLIGWDLLLEYALIVAVVAIGWSGYVQSALASIG---- 142 Query: 150 HDVSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSIIVAI 209 V LP A +GH+ N+ A + ++ L A N+ +VAI Sbjct: 143 --VDLP-VWAKGAIGTGEGHV------FNVVAALVTLGVSALLIFRTEWGARFNTFVVAI 193 Query: 210 KVTVILLFIAFATKYINPDNWHPFIP----ASEGASKYGWAGVGRAAAIVFFSYIGFDAV 265 KV + L I Y+ P+NW PFIP S+G +G+ GV AAA+VFF+ G+D + Sbjct: 194 KVAAVALVIGVGAFYVKPENWVPFIPERIVGSDGVGHFGFQGVATAAAVVFFAVFGYDTL 253 Query: 266 STAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPEPVSTALDNYPS 325 +TAA E+KNPQRD+P ++ SL + +Y+ V+ +LTGIA + L T PV+ A Sbjct: 254 TTAAEESKNPQRDLPRAVLLSLGISMAMYLAVSMVLTGIAHYTTLKTDAPVADAFKGL-G 312 Query: 326 LHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTVV 385 LHW+ + V + AV GL SV+ ++G RI++++ARDGL+P F + H ++ TPH T+V Sbjct: 313 LHWVALTVSVSAVFGLISVLFAFMLGATRIWFALARDGLLPGWFAKPHPRYGTPHRPTIV 372 Query: 386 VGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVPVPWIVCP 445 +GV A + GL I + ++V +G L AF +C VL+LR +P+L RAFR P+ ++ Sbjct: 373 LGVFTALVAGLLPIEEVAKLVNIGVLSAFIVICSSVLILRKRKPDLYRAFRTPLVPLIPL 432 Query: 446 LGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKLRK 489 +G + L + W L W++IG +YF YG HSKL K Sbjct: 433 VGIGFSIWLLAELPWVTWEVFLIWVSIGLVVYFGYGIRHSKLEK 476 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: 721 Number of extensions: 37 Number of successful extensions: 6 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: 477 Length adjustment: 34 Effective length of query: 458 Effective length of database: 443 Effective search space: 202894 Effective search space used: 202894 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 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