Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate WP_102938052.1 B1812_RS04230 amino acid permease
Query= uniprot:A0A1I1Y8J0 (492 letters) >NCBI__GCF_002117405.1:WP_102938052.1 Length = 481 Score = 447 bits (1150), Expect = e-130 Identities = 226/462 (48%), Positives = 311/462 (67%), Gaps = 9/462 (1%) Query: 26 EATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCY 85 E LKRAL L+ +GIG IIGAGIFV+TGQAAA++AGP + +SF+ +G+AC ALCY Sbjct: 26 ENGLKRALGWASLMAMGIGGIIGAGIFVLTGQAAADYAGPGVTISFLLSGLACTFVALCY 85 Query: 86 AEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALIS 145 AE AA++P +GS Y+Y+Y TLGE AW +GW+LVLEY ATVA GW+GYFN+++ Sbjct: 86 AELAALIPAAGSTYTYTYVTLGEIFAWIIGWNLVLEYAAGAATVAVGWAGYFNRVMQ--- 142 Query: 146 GWIGHDVSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSI 205 G + LP+ L +A F G+F N+PA AII +T L G ++S+F N+I Sbjct: 143 ---GLGIHLPEALTSAYFANAHSIGGTHGVF-NVPAAAIILLLTALLMRGTSESSFFNNI 198 Query: 206 IVAIKVTVILLFIAFATKYINPDNWHPFIPA-SEGASKYGWAGVGRAAAIVFFSYIGFDA 264 IV IKV V+L+ I +++ NW P IP ++ +GW+GV R A++VFF+YIGFD Sbjct: 199 IVVIKVMVVLVVIFVGAAHVDAANWTPLIPENTDHFGHFGWSGVVRGASVVFFAYIGFDG 258 Query: 265 VSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPEPVSTALDNYP 324 VSTAA EA PQRD+PIGI+GSL++CTILY+ VA + TG+ ++ LG P+P++ +D Sbjct: 259 VSTAAQEAHTPQRDVPIGILGSLVICTILYVAVAAVATGVVSYKELGVPDPMALVMDR-T 317 Query: 325 SLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTV 384 + WL +V +GA+ GL++ +L++L GQ RIFY+MA+DGL+P VF +H +RTP V Sbjct: 318 GVAWLSWVVKLGAIAGLTTAILLLLFGQTRIFYAMAQDGLLPKVFAAVHPVWRTPAVSQA 377 Query: 385 VVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVPVPWIVC 444 +VGV A GLF I +L EMV++GTL AFA VC VL LR ++P++ R FR P + Sbjct: 378 LVGVFVALAAGLFPINILDEMVSIGTLAAFALVCGAVLHLRRSQPDMHRPFRAPGIPAMP 437 Query: 445 PLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSK 486 LG +C+AL + LE W ++ W AIG AIYF YG H+K Sbjct: 438 LLGIASCLALMVALPLETWLRLIVWTAIGMAIYFFYGVKHAK 479 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: 745 Number of extensions: 44 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: 481 Length adjustment: 34 Effective length of query: 458 Effective length of database: 447 Effective search space: 204726 Effective search space used: 204726 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