Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate WP_092483642.1 BM299_RS10185 amino acid permease
Query= uniprot:A0A1I1Y8J0 (492 letters) >NCBI__GCF_900115975.1:WP_092483642.1 Length = 484 Score = 398 bits (1023), Expect = e-115 Identities = 209/452 (46%), Positives = 285/452 (63%), Gaps = 23/452 (5%) Query: 38 LVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCYAEFAAMLPVSGS 97 L LG+GA+IG GIFV+TG AAA +AGP +V SF+ +GIA LAA+ YAE A +P +GS Sbjct: 32 LTALGVGAVIGTGIFVLTGVAAANYAGPGVVFSFILSGIAATLAAMVYAELGAAIPSAGS 91 Query: 98 AYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALISGWIGHDVSLPQT 157 AY++SY +LGE +AW VGW+L+LEYL V+ GWS Y LL + ++LP Sbjct: 92 AYTFSYVSLGEIIAWLVGWNLILEYLVAAGAVSIGWSSYMGDLLQSVG------ITLPAA 145 Query: 158 LAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSIIVAIKVTVILLF 217 ++PF DG I +NLPA I+ ITGL G S N IIV K+ I LF Sbjct: 146 FTSSPF---DGGI------VNLPAALIVLVITGLIITGTQHSTTANKIIVVAKLAAIALF 196 Query: 218 IAFATKYINPDNWHPFIPASEGASKYGWAGVGRAAAIVFFSYIGFDAVSTAAGEAKNPQR 277 IA ++INP NW P +P YG +GV AAIVFF+YIGFDAV+TA+ E KNPQR Sbjct: 197 IALGVQHINPANWRPVLP-------YGISGVFHGAAIVFFAYIGFDAVATASEEVKNPQR 249 Query: 278 DMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPEPVSTALDNYPSLHWLQIIVVIGA 337 D+P GII +L++ T+LYI+VAGILTG+ + L T PV+TAL + W +V +GA Sbjct: 250 DLPRGIIWTLVISTLLYIVVAGILTGMVKYTNLNTASPVATALLR-AGIPWASALVSVGA 308 Query: 338 VTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTVVVGVLAAALGGLF 397 + GL+SV+LV + GQ RIF++MARD L+P +F +H + RTP ++++GVL A +G Sbjct: 309 LAGLTSVLLVAMYGQSRIFFAMARDDLLPPIFDWLHPRLRTPVWDSIIIGVLVALIGAFL 368 Query: 398 NIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVPVPWIVCPLGALACMALFLQ 457 IG++ E+ +GTL AF V G ++LR T P+L R FR+P + L ++ L + Sbjct: 369 PIGLVAELANIGTLTAFIAVSTGAIILRRTNPDLRRPFRLPWMPAIPVLTIISAGYLAIN 428 Query: 458 SFLEHWRWMLAWIAIGQAIYFLYGYSHSKLRK 489 W +AW+AIG +Y+LYGY SKL + Sbjct: 429 LPPLTWVRFIAWVAIGLVVYWLYGYRKSKLAR 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: 764 Number of extensions: 35 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: 484 Length adjustment: 34 Effective length of query: 458 Effective length of database: 450 Effective search space: 206100 Effective search space used: 206100 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