Align Amino acid transporter (characterized, see rationale)
to candidate Ga0059261_1053 Ga0059261_1053 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= uniprot:A0A0H3C3Q5 (483 letters) >FitnessBrowser__Korea:Ga0059261_1053 Length = 512 Score = 429 bits (1103), Expect = e-124 Identities = 234/497 (47%), Positives = 315/497 (63%), Gaps = 49/497 (9%) Query: 13 RRKAIDTITAGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGLAGPGVILSFL 72 R K +D I A A+ L ++L L LG+GA++GTGI+ LT A AGPG++LSF+ Sbjct: 5 RVKPLDAILAT-AEKKSLHRSLGAFQLTMLGIGAVIGTGIFVLTAEAAQKAGPGMMLSFV 63 Query: 73 IAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVG 132 IAG VCA AALCYAE++ M+P SGSAYTYSYA MGE +AW VGW+LILEY + AV+VG Sbjct: 64 IAGVVCAVAALCYAEMAAMVPVSGSAYTYSYAVMGELIAWMVGWALILEYAVAAGAVSVG 123 Query: 133 WSAHAHGLFK---MIGFPDALLAGPHQGGLINMPAVFISMAVAGLLALGTRESATVNMVL 189 WS + GL + + PDAL+ GP+ GG+IN+PA+ I+ V LL +GT+ESA VN VL Sbjct: 124 WSGYVVGLIENAFALDIPDALVRGPYDGGIINLPAMLIAGLVTWLLVIGTKESAFVNSVL 183 Query: 190 VFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFFAF 249 V VK+ AL +F++L +P N+ +F PF P GF GV AAA+ IFFA+ Sbjct: 184 VLVKVSALSLFIILAIPVMNMQNFEPFSPLGF--------------AGVSAAAASIFFAY 229 Query: 250 YGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIG---------------- 293 GFDAVSTAAEETKNP+R++ IG++GS+A+CT Y++VAA IG Sbjct: 230 VGFDAVSTAAEETKNPQRNMPIGLIGSLAICTIFYLLVAAGVIGSVGAQPILGPDGAALP 289 Query: 294 ---------------ASRTEVFSKSEAPLVFILESLNHGKIAQLVALAAVIALPTVILAF 338 A+ E S+ L + L + +I L+ LAA +ALP+VIL Sbjct: 290 PGSTELTKACVETAAATGKEAVVCSKEALAWTLREIGWPQIGNLIGLAAGLALPSVILMM 349 Query: 339 MYGQSRIFFVMARDGLLPRALSKVNAKTGTPVMMTLLTGVLAAVISGLLSLKDIAELANA 398 M+GQ+RIFFVM+RDGLLP SKV+ K TP ++T+LTGV A+ + + +A+++N+ Sbjct: 350 MFGQTRIFFVMSRDGLLPAVFSKVHPKFHTPHVITILTGVFVALFAAFFPVGKLADISNS 409 Query: 399 GTLWAFIAVGASVILLRLREPNRPRVFSTPLWPIVAPAGILGCLYLFLSLPGKTQLYFLY 458 GTL+AF AV +V++LR +P+R R F TPL I AP ILGC YLF SL T++ F+ Sbjct: 410 GTLFAFAAVSIAVLVLRRTDPDRKRPFRTPLIIITAPIAILGCAYLFYSLGHDTKMMFVG 469 Query: 459 AHLIGAVVYLAYGMRKS 475 +G +VY Y RKS Sbjct: 470 WAALGLLVYFGYSRRKS 486 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: 736 Number of extensions: 34 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: 483 Length of database: 512 Length adjustment: 34 Effective length of query: 449 Effective length of database: 478 Effective search space: 214622 Effective search space used: 214622 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