Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate BPHYT_RS01785 BPHYT_RS01785 amino acid permease
Query= uniprot:A0A1I1Y8J0 (492 letters) >FitnessBrowser__BFirm:BPHYT_RS01785 Length = 463 Score = 404 bits (1039), Expect = e-117 Identities = 218/464 (46%), Positives = 291/464 (62%), Gaps = 21/464 (4%) Query: 27 ATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCYA 86 A LK+AL A L LG+GAIIG GIFV+TG A + AGPA+++SF+ A IAC AAL YA Sbjct: 20 AGLKKALGALDLTFLGVGAIIGTGIFVLTGTGAVQ-AGPALMISFLIAAIACGFAALAYA 78 Query: 87 EFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALISG 146 EFA+ +PV+GS Y+YSYATLGE AW +GW L+LEY + V+ GWSGY LL+ Sbjct: 79 EFASTIPVAGSIYTYSYATLGELAAWIIGWDLMLEYGLATSAVSVGWSGYLQSLLS---- 134 Query: 147 WIGHDVSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSII 206 G VSLP L AAP G + NLPA ++ AIT L VG+ +SA +N+++ Sbjct: 135 --GFGVSLPVALTAAP-----GALPGHDTLFNLPAFLVMMAITALLSVGVRESARINNVM 187 Query: 207 VAIKVTVILLFIAFATKYINPDNWHPFIPASEGASKYGWAGVGRAAAIVFFSYIGFDAVS 266 VAIKV V+LL I ++ P NWHPF+P GW GV AAA++FF++IGFD+VS Sbjct: 188 VAIKVVVVLLVIGVGVFHVTPANWHPFMPN-------GWNGVFGAAAVMFFAFIGFDSVS 240 Query: 267 TAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIA-DFRLLGTPEPVSTALDNYPS 325 +AA E K+P+RD+PIGII SL +C +LY+ VA ++TGI + PVS AL Sbjct: 241 SAAEEVKDPKRDLPIGIIASLGVCAVLYVAVAAVVTGIVPSAQFANISHPVSYALQ-VAG 299 Query: 326 LHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTVV 385 W+ + +GAV G+ +V+LVM GQ R+ ++M+RDGL+P R+H +F TP T + Sbjct: 300 EKWVAGFIDLGAVLGMLTVILVMAYGQTRVIFAMSRDGLLPERLSRVHPRFATPFFTTWL 359 Query: 386 VGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVPVPWIVCP 445 VG+ +G L + VL E++ +GTL AF+ V I VLVLR T P+LPRAFR P +V Sbjct: 360 VGIFFGLIGALVPLNVLAELINIGTLAAFSMVSIAVLVLRKTHPDLPRAFRCPGVPVVPV 419 Query: 446 LGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKLRK 489 L AC+ L + W + W+ +G IYF Y HSKL K Sbjct: 420 LAVAACLFLMVNLQAVTWVAFVVWLLVGMVIYFGYSRRHSKLSK 463 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: 726 Number of extensions: 43 Number of successful extensions: 7 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: 463 Length adjustment: 34 Effective length of query: 458 Effective length of database: 429 Effective search space: 196482 Effective search space used: 196482 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