Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate RR42_RS01585 RR42_RS01585 amino acid permease
Query= uniprot:A0A1I1Y8J0 (492 letters) >FitnessBrowser__Cup4G11:RR42_RS01585 Length = 464 Score = 409 bits (1052), Expect = e-119 Identities = 224/463 (48%), Positives = 299/463 (64%), Gaps = 27/463 (5%) Query: 29 LKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCYAEF 88 LK+ L L+L+GIGAIIG GIFV+TG A AGPA+ +SFV A +AC AALCYAEF Sbjct: 21 LKKVLGPVDLILMGIGAIIGTGIFVLTGTGALT-AGPALTVSFVIAALACGFAALCYAEF 79 Query: 89 AAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALISGWI 148 A+ +PVSGS Y+YSYATLGE VAW +GW L+LEY + V+ GWSGYF L+A Sbjct: 80 ASAIPVSGSIYTYSYATLGEIVAWMIGWDLLLEYGLATSAVSVGWSGYFQSLMA------ 133 Query: 149 GHDVSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSIIVA 208 G + LP L AAP G + NLPA I+ IT + G+ +SA +N+++VA Sbjct: 134 GFGIHLPAMLTAAP-----GAVPGVQTLFNLPAAVIMLLITWVVSYGVRESARLNNVMVA 188 Query: 209 IKVTVILLFIAFATKYINPDNWHPFIPASEGASKYGWAGVGRAAAIVFFSYIGFDAVSTA 268 +K+ V+LLFI ++ P NWHPF P +G GV AAA+VFF++IGFDAV++A Sbjct: 189 VKIAVVLLFIGVGVWHVKPANWHPFAP-------FGLDGVFNAAALVFFAFIGFDAVTSA 241 Query: 269 AGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADF-RLLGTPEPVSTALDNYPSLH 327 A E +NP+RD+PIGIIGSL +CT+LY+ VA I+TGI F + G PVS AL Y + Sbjct: 242 AEEVRNPRRDLPIGIIGSLAVCTVLYVTVAAIMTGIVPFAKFAGIDHPVSLALQ-YAGEN 300 Query: 328 WLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTVVVG 387 W+ V +GA+ G+++V+LVM GQ RI ++M+RDGL+P +H TP T VG Sbjct: 301 WVAGFVDLGAILGMTTVILVMTFGQTRIIFAMSRDGLLPERLSTVHPVHATPFFATWTVG 360 Query: 388 VLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVP-VPWIVCPL 446 ++ A + + VL E++ +GTL AF + + VLVLR TRP+LPRAFR P VP V PL Sbjct: 361 IVFAFIAAFVPLNVLAELINIGTLSAFTLISVAVLVLRKTRPDLPRAFRCPGVP--VVPL 418 Query: 447 GALACMALFLQSFLEHWRWM--LAWIAIGQAIYFLYGYSHSKL 487 ++ LFL + L+ W+ LAW+AIG AIYFLY ++ L Sbjct: 419 LSVG-FCLFLMAHLQALTWVAFLAWLAIGLAIYFLYARRNAVL 460 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: 716 Number of extensions: 38 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: 464 Length adjustment: 34 Effective length of query: 458 Effective length of database: 430 Effective search space: 196940 Effective search space used: 196940 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: 51 (24.3 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