Align Amino acid transporter (characterized, see rationale)
to candidate N515DRAFT_2924 N515DRAFT_2924 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= uniprot:A0A0H3C3Q5 (483 letters) >FitnessBrowser__Dyella79:N515DRAFT_2924 Length = 492 Score = 336 bits (861), Expect = 1e-96 Identities = 196/469 (41%), Positives = 273/469 (58%), Gaps = 31/469 (6%) Query: 30 LKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGL-AGPGVILSFLIAGAVCACAALCYAEL 88 LK+ L+ HLV LG+GAI+G GI+ +TG A AGP ++LSF+ AG CA AALCYAE Sbjct: 29 LKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAALCYAEF 88 Query: 89 STMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVGWSAHAHGLFKMI---- 144 + M+P SGSAY+YSYA +GE VAWFVGWSL+LEY A VA GWS + + L +I Sbjct: 89 AAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLALISGWI 148 Query: 145 ----GFPDALLAGPH---------QGGLINMPAVFISMAVAGLLALGTRESATVNMVLVF 191 P L A P G IN+PAV I A+ GL +G +SA VN ++V Sbjct: 149 GHDVSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFVNSIIVA 208 Query: 192 VKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFFAFYG 251 +K+ +++F+ N ++ PF+P EG A+ GV AA+++FF++ G Sbjct: 209 IKVTVILLFIAFATKYINPDNWHPFIP------ASEG-ASKYGWAGVGRAAAIVFFSYIG 261 Query: 252 FDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPLVFIL 311 FDAVSTAA E KNP+RD+ IGI+GS+ +CT +Y+IVA + G + + E P+ L Sbjct: 262 FDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPE-PVSTAL 320 Query: 312 E---SLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGT 368 + SL+ +I +V + AV L +V+L + GQ RIF+ MARDGL+P +++ K T Sbjct: 321 DNYPSLHWLQI--IVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRT 378 Query: 369 PVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFSTP 428 P + T++ GVLAA + GL ++ + E+ GTL AF V V++LR P PR F P Sbjct: 379 PHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVP 438 Query: 429 LWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVL 477 + IV P G L C+ LFL + + L IG +Y YG S L Sbjct: 439 VPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQAIYFLYGYSHSKL 487 Lambda K H 0.326 0.138 0.415 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: 675 Number of extensions: 43 Number of successful extensions: 6 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: 483 Length of database: 492 Length adjustment: 34 Effective length of query: 449 Effective length of database: 458 Effective search space: 205642 Effective search space used: 205642 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 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