Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate WP_091525815.1 BM253_RS14680 amino acid permease
Query= uniprot:A0A1I1Y8J0 (492 letters) >NCBI__GCF_900115115.1:WP_091525815.1 Length = 637 Score = 324 bits (831), Expect = 5e-93 Identities = 181/468 (38%), Positives = 269/468 (57%), Gaps = 51/468 (10%) Query: 4 NLFATTQISPASADLPGGGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHA 63 N+F ++ A+L E+ L + L+ + L+ GI AI+GAG+F GQA+ + Sbjct: 2 NIFRKKNVTDILAELQANEGKKES-LGKFLSQKDLIFFGIAAIVGAGVFSTIGQASFD-G 59 Query: 64 GPAIVLSFVFAGIACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYL 123 GPA++ F+F +AC AA+ YAEFA+M+PVSGSAY+YSY GE +AW +GWSL++EY Sbjct: 60 GPAVIFLFMFTALACGFAAMAYAEFASMVPVSGSAYTYSYVAFGEVIAWIIGWSLIMEYA 119 Query: 124 FTVATVAAGWSGYFNKLLALISGWIGHDVSLPQTLAAAPFTVVDGHIQATGMFIN----- 178 T+A WS YF LL+ D+ LPQ + + G A + N Sbjct: 120 VGNITLAISWSDYFTGLLS------NMDIHLPQWIQMDYLSANKGFNDAVALMANGKSFE 173 Query: 179 ---------------------------LPAVAIIAAITGLCYVGITQSAFVNSIIVAIKV 211 +PA+AII IT L Y G+ +S ++I+V +K+ Sbjct: 174 NLPNNLQLAHIAWTTAPQIGSFHFVADIPALAIIVLITWLVYRGMKESRNASNIMVYVKL 233 Query: 212 TVILLFIAFATKYINPDNWHPFIPASEGASKYGWAGVGRAAAIVFFSYIGFDAVSTAAGE 271 VI L + Y++ DN+ PF P G +GV + + VFF+YIGFDA+ST A E Sbjct: 234 AVIALVLIVGIFYVDTDNFDPFAP-------NGLSGVLKGVSAVFFAYIGFDAISTTAEE 286 Query: 272 AKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPEPVSTALDNYPSLHWLQI 331 KNPQRD+P +I S+I+CT+LYI +A +LTG+ +++ L +P++ D +L W Sbjct: 287 CKNPQRDLPRSMIWSIIICTLLYIAIALVLTGMVNYKQLNVGDPLAYVFDQV-NLKWFAG 345 Query: 332 IVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTVVVGVLAA 391 IV + AV ++SV+LV MGQPRI+ SM+RDGL+P F ++H K+RTP T+V G + A Sbjct: 346 IVAVSAVVAMASVLLVFQMGQPRIWMSMSRDGLLPKKFSKVHPKYRTPSFATIVTGFVVA 405 Query: 392 ALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRA-FRVP 438 N+ ++ ++ ++GTL AF+ VC GVLVL+ ++PR FR+P Sbjct: 406 VPALFMNLTMVTDLCSIGTLFAFSLVCAGVLVLQ--DKDIPRGKFRIP 451 Score = 34.3 bits (77), Expect = 1e-05 Identities = 14/42 (33%), Positives = 23/42 (54%) Query: 446 LGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKL 487 LG + C+ + + + +W + W+ IG IYF Y +SKL Sbjct: 593 LGLICCIYMMAELTIWNWLYFSIWLIIGLLIYFSYSRFNSKL 634 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: 851 Number of extensions: 46 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 492 Length of database: 637 Length adjustment: 36 Effective length of query: 456 Effective length of database: 601 Effective search space: 274056 Effective search space used: 274056 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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