Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate CA265_RS17395 CA265_RS17395 amino acid transporter
Query= uniprot:A0A1I1Y8J0 (492 letters) >FitnessBrowser__Pedo557:CA265_RS17395 Length = 483 Score = 424 bits (1090), Expect = e-123 Identities = 214/469 (45%), Positives = 306/469 (65%), Gaps = 14/469 (2%) Query: 25 GEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALC 84 GE +LKR L +L+L+G+G +GAG+F ITG AAA H+GPA+ LSFV A + C AALC Sbjct: 16 GEGSLKRTLGPINLILIGVGLTLGAGLFSITGLAAANHSGPAVTLSFVIAALGCGFAALC 75 Query: 85 YAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALI 144 YAEFA+M+PV+GSAY+YSYAT+GE AW +GW LVLEY ATVA WS Y K LA + Sbjct: 76 YAEFASMIPVAGSAYTYSYATMGELFAWIIGWDLVLEYSVGCATVAISWSQYLTKFLASL 135 Query: 145 SGWIGHDVSLPQTLAAAPF---TVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAF 201 + LP L +PF + DG IN+PA ++ +T + G SA Sbjct: 136 ------HIYLPPQLTLSPFETAKLADG--STVNGIINIPAALVVVLMTAILIRGTKGSAI 187 Query: 202 VNSIIVAIKVTVILLFIAFATKYINPDNWHPFIPASEGA-SKYGWAGVGRAAAIVFFSYI 260 VN IIV +KV V+L+FIA +YI+P N+HP+IP + G ++GW+GV R A +VFF +I Sbjct: 188 VNGIIVFLKVGVVLVFIALGWQYIDPANYHPYIPENTGTFGQFGWSGVLRGAGLVFFVFI 247 Query: 261 GFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFR-LLGTPEPVSTA 319 GFDAV+ +A E KNP RD+PIGIIGSL++CT+L+ + ++TG+A+++ + PV+ A Sbjct: 248 GFDAVAASAQETKNPARDLPIGIIGSLLVCTVLFGLFGHVMTGLANYKEFANSGAPVAIA 307 Query: 320 LDNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTP 379 ++ P WL +++ + G +SV+L+ LM Q R+FYS+++DGL+P +F +H KF+TP Sbjct: 308 IEKTP-YAWLSQAIILAILIGYTSVILIDLMAQSRMFYSISKDGLLPKMFSDVHAKFKTP 366 Query: 380 HVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVPV 439 + +++ V + V+GEM ++GTLLAF VC+G+L+LR T PE R F+VP Sbjct: 367 YKSNIILCVFIGLFAAFVPMNVVGEMTSIGTLLAFLMVCVGILILRKTNPEAKRPFKVPF 426 Query: 440 PWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKLR 488 ++ LG L C+A+ + E W + W+ IG AIYF YG +SKL+ Sbjct: 427 VPLIPILGILTCIAMMVFLPWETWLRLAVWLIIGLAIYFWYGKKNSKLK 475 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: 733 Number of extensions: 35 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: 492 Length of database: 483 Length adjustment: 34 Effective length of query: 458 Effective length of database: 449 Effective search space: 205642 Effective search space used: 205642 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