Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate CA265_RS15145 CA265_RS15145 amino acid permease
Query= uniprot:A0A1I1Y8J0 (492 letters) >FitnessBrowser__Pedo557:CA265_RS15145 Length = 649 Score = 329 bits (844), Expect = 2e-94 Identities = 189/475 (39%), Positives = 269/475 (56%), Gaps = 49/475 (10%) Query: 1 MLKNLFATTQISPASADLPGGGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAA 60 M + LF IS D G E TL + L R L GI AIIGAGIF G+A+A Sbjct: 1 MFEKLFRKKSISKILQDAAKGYGDHENTLHKTLGVRDLTAFGIAAIIGAGIFSTIGKASA 60 Query: 61 EHAGPAIVLSFVFAGIACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVL 120 + GPA++ F+F +AC+ AA YAEFA+M+PVSGSAY+YSY GE VAW +GWSL++ Sbjct: 61 D-GGPAVIFLFIFTAVACSFAAFAYAEFASMVPVSGSAYTYSYVAFGELVAWIIGWSLIM 119 Query: 121 EYLFTVATVAAGWSGYFNKLLALIS----GWIGHDVSLPQTLAAAPFTVVDGHIQATGMF 176 EY TVA WS YF LL+ I G G + +P + + +GH A + Sbjct: 120 EYSIGNITVAISWSDYFTGLLSTIKIPPLGIEG--IHVPDWMTMDYLSAYNGHKHAEALL 177 Query: 177 I--------------------------------NLPAVAIIAAITGLCYVGITQSAFVNS 204 ++PA+ II IT L Y G+ +S ++ Sbjct: 178 AAGKNLADLDSATALANNAWLTAPKIGSFHLVADIPALGIIILITWLIYRGMKESRNASN 237 Query: 205 IIVAIKVTVILLFIAFATKYINPDNWHPFIPASEGASKYGWAGVGRAAAIVFFSYIGFDA 264 +V +K+ VILL +A Y++ NW PF P G +GV + + VFF+YIGFDA Sbjct: 238 AMVVVKLAVILLVLAVGIFYVDTKNWDPFAPN-------GVSGVLKGVSAVFFAYIGFDA 290 Query: 265 VSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPEPVSTALDNYP 324 +ST A E KNPQRD+P G++ ++I+CTILY+ +A +LTGI L +P++ D Sbjct: 291 ISTTAEECKNPQRDLPRGMMWAIIICTILYVAIALVLTGIVKSDTLAVGDPLAFVFDQI- 349 Query: 325 SLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPHVGTV 384 +L + I+ + AV ++SV+LV MGQPRI+ SM+RDGL+P F +IH K++TP T+ Sbjct: 350 NLKLMSGIIAVSAVFAMASVLLVFQMGQPRIWMSMSRDGLLPKSFSKIHPKYKTPSFATI 409 Query: 385 VVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRA-FRVP 438 VVG + A N+ ++ ++ ++GTL AF VC GVLVL+ RP++ R F++P Sbjct: 410 VVGFVVAVPSLFMNLTIVTDLCSIGTLFAFVLVCAGVLVLQ-NRPDVQRGKFKIP 463 Score = 43.9 bits (102), Expect = 2e-08 Identities = 16/44 (36%), Positives = 26/44 (59%) Query: 446 LGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKLRK 489 LG ++C+ + + + +W W+ +G +YF YGY HSKL K Sbjct: 603 LGLISCLYMMCELGISNWIGFGIWLVVGLVVYFAYGYRHSKLAK 646 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: 897 Number of extensions: 45 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 492 Length of database: 649 Length adjustment: 36 Effective length of query: 456 Effective length of database: 613 Effective search space: 279528 Effective search space used: 279528 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 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