Align Amino acid transporter (characterized, see rationale)
to candidate N515DRAFT_0606 N515DRAFT_0606 basic amino acid/polyamine antiporter, APA family
Query= uniprot:A0A0H3C3Q5 (483 letters) >FitnessBrowser__Dyella79:N515DRAFT_0606 Length = 477 Score = 320 bits (819), Expect = 9e-92 Identities = 185/477 (38%), Positives = 278/477 (58%), Gaps = 13/477 (2%) Query: 8 VSFWTRRKAIDTITAGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGL-AGPG 66 VS R K+++ + A ++ L L A+G+G I+G G++ L G A L AGP Sbjct: 4 VSKLVRHKSVEQLQADVGKRGDFRRVLGLWQLTAIGIGGIIGVGVFVLAGQQAALNAGPA 63 Query: 67 VILSFLIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVC 126 V +SFLIAG A AALCYAE + +IP +GSAYTY YA +GE AW +GW L+LEY L+ Sbjct: 64 VAISFLIAGIASAAAALCYAEFAGLIPVTGSAYTYGYAVLGELAAWLIGWDLLLEYALIV 123 Query: 127 AAVAVGWSAHAHGLFKMIGFPDALLA----GPHQGGLINMPAVFISMAVAGLLALGTRES 182 A VA+GWS + IG + A G +G + N+ A +++ V+ LL T Sbjct: 124 AVVAIGWSGYVQSALASIGVDLPVWAKGAIGTGEGHVFNVVAALVTLGVSALLIFRTEWG 183 Query: 183 ATVNMVLVFVKIIALIVFVVLCLPAFNLA--HFTPFMPNGFQAHVPEGAAADAAKVGVMA 240 A N +V +K+ A V +V+ + AF + ++ PF+P V GV Sbjct: 184 ARFNTFVVAIKVAA--VALVIGVGAFYVKPENWVPFIPERI---VGSDGVGHFGFQGVAT 238 Query: 241 AASLIFFAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVF 300 AA+++FFA +G+D ++TAAEE+KNP+RDL ++ S+ + A+Y+ V+ V G + Sbjct: 239 AAAVVFFAVFGYDTLTTAAEESKNPQRDLPRAVLLSLGISMAMYLAVSMVLTGIAHYTTL 298 Query: 301 SKSEAPLVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALS 360 K++AP+ + L +A V+++AV L +V+ AFM G +RI+F +ARDGLLP + Sbjct: 299 -KTDAPVADAFKGLGLHWVALTVSVSAVFGLISVLFAFMLGATRIWFALARDGLLPGWFA 357 Query: 361 KVNAKTGTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPN 420 K + + GTP T++ GV A+++GLL ++++A+L N G L AFI + +SV++LR R+P+ Sbjct: 358 KPHPRYGTPHRPTIVLGVFTALVAGLLPIEEVAKLVNIGVLSAFIVICSSVLILRKRKPD 417 Query: 421 RPRVFSTPLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVL 477 R F TPL P++ GI ++L LP T FL IG VVY YG+R S L Sbjct: 418 LYRAFRTPLVPLIPLVGIGFSIWLLAELPWVTWEVFLIWVSIGLVVYFGYGIRHSKL 474 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: 676 Number of extensions: 38 Number of successful extensions: 4 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: 477 Length adjustment: 34 Effective length of query: 449 Effective length of database: 443 Effective search space: 198907 Effective search space used: 198907 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