Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate Ga0059261_1577 Ga0059261_1577 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= uniprot:A0A1I1Y8J0 (492 letters) >FitnessBrowser__Korea:Ga0059261_1577 Length = 470 Score = 347 bits (890), Expect = e-100 Identities = 200/488 (40%), Positives = 278/488 (56%), Gaps = 37/488 (7%) Query: 1 MLKNLFATTQISPASADLPGGGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAA 60 M LF T ++ A+ P E L L+ HLV LG+GAI+G GI + G A Sbjct: 1 MAGGLFRTKRVKDAAEQAP------EHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAG 54 Query: 61 EHAGPAIVLSFVFAGIACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVL 120 + AGPA+++SFV AG CA AAL YAE A M+P SGSAY+YSYA LGE +AW VGWSL+L Sbjct: 55 K-AGPAVIMSFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLIL 113 Query: 121 EYLFTVATVAAGWSGYFNKLLALISGWIGHDVSLPQTLAAAPFTVVDGHIQATGMFINLP 180 EY V+TVA GWSGY L+ W G +P L A P A G+ +NLP Sbjct: 114 EYSLVVSTVAVGWSGY---AAPLLHAWTG----MPLELMAGP--------HANGI-VNLP 157 Query: 181 AVAIIAAITGLCYVGITQSAFVNSIIVAIKVTVILLFIAFATKYINPDNWHPFIP----- 235 A+ IIA + GL +G +SA +N+ +V +K+ + +F+A A Y N N PF P Sbjct: 158 AIFIIAVVAGLLCLGTKESATLNAALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAK 217 Query: 236 --ASEGASKYGWAGVGRAAAIVFFSYIGFDAVSTAAGEAKNPQRDMPIGIIGSLILCTIL 293 + +G + GV AAAI+FF++ GFDA+STAA E KNP RD+ IGI+GS+I C + Sbjct: 218 TISPDGVER----GVMAAAAIIFFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAI 273 Query: 294 YIIVAGILTGIADF-RLLGTPEPVSTALDNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQ 352 Y++VA G F +PEP++ L + + + V A+ L +V+L L GQ Sbjct: 274 YMLVAVAAVGATPFTHFANSPEPLALILRDLGRPGFATFLAV-SAIIALPTVLLGFLFGQ 332 Query: 353 PRIFYSMARDGLIPAVFGRIHQKFRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLL 412 RIF++MARDG++P ++ K +P T+ + A + GL I + + GTL Sbjct: 333 SRIFFTMARDGMLPIGLAKV-SKRGSPVRITLFTAAIVAVIAGLLPIDEIAALANAGTLA 391 Query: 413 AFATVCIGVLVLRYTRPELPRAFRVPVPWIVCPLGALACMALFLQSFLEHWRWMLAWIAI 472 AF V + ++VLR P++PR FR P+ W+V + L C+ LF ++ W LAW A+ Sbjct: 392 AFTAVAVCMMVLRVRAPDMPRMFRTPLWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNAL 451 Query: 473 GQAIYFLY 480 G IYF Y Sbjct: 452 GVVIYFAY 459 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: 730 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: 470 Length adjustment: 34 Effective length of query: 458 Effective length of database: 436 Effective search space: 199688 Effective search space used: 199688 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