Align Amino acid transporter (characterized, see rationale)
to candidate Ga0059261_1577 Ga0059261_1577 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= uniprot:A0A0H3C3Q5 (483 letters) >FitnessBrowser__Korea:Ga0059261_1577 Length = 470 Score = 528 bits (1360), Expect = e-154 Identities = 273/450 (60%), Positives = 334/450 (74%), Gaps = 6/450 (1%) Query: 22 AGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGLAGPGVILSFLIAGAVCACA 81 A A H+L TLSWPHLVALGVGAIVGTGI TL GVGAG AGP VI+SF+IAGA+CACA Sbjct: 15 AEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGKAGPAVIMSFVIAGAICACA 74 Query: 82 ALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVGWSAHAHGLF 141 AL YAE++TM+PASGSAY YSYA +GE +AW VGWSLILEY+LV + VAVGWS +A L Sbjct: 75 ALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAVGWSGYAAPLL 134 Query: 142 -KMIGFPDALLAGPHQGGLINMPAVFISMAVAGLLALGTRESATVNMVLVFVKIIALIVF 200 G P L+AGPH G++N+PA+FI VAGLL LGT+ESAT+N LV VKIIAL VF Sbjct: 135 HAWTGMPLELMAGPHANGIVNLPAIFIIAVVAGLLCLGTKESATLNAALVVVKIIALAVF 194 Query: 201 VVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFFAFYGFDAVSTAAE 260 V + LP FN A+ PF P GF + + D + GVMAAA++IFFAFYGFDA+STAAE Sbjct: 195 VAVALPYFNGANLEPFAPFGFAKTI----SPDGVERGVMAAAAIIFFAFYGFDAISTAAE 250 Query: 261 ETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPLVFILESLNHGKIA 320 ETKNP RDL IGIVGSM C AIYM+VA ++GA+ F+ S PL IL L A Sbjct: 251 ETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALILRDLGRPGFA 310 Query: 321 QLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGTPVMMTLLTGVLA 380 +A++A+IALPTV+L F++GQSRIFF MARDG+LP L+KV +K G+PV +TL T + Sbjct: 311 TFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKV-SKRGSPVRITLFTAAIV 369 Query: 381 AVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFSTPLWPIVAPAGILG 440 AVI+GLL + +IA LANAGTL AF AV +++LR+R P+ PR+F TPLW +V +LG Sbjct: 370 AVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWWLVGAIAVLG 429 Query: 441 CLYLFLSLPGKTQLYFLYAHLIGAVVYLAY 470 C+YLF SLP KTQL+FL + +G V+Y AY Sbjct: 430 CIYLFFSLPVKTQLWFLAWNALGVVIYFAY 459 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: 790 Number of extensions: 47 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: 470 Length adjustment: 33 Effective length of query: 450 Effective length of database: 437 Effective search space: 196650 Effective search space used: 196650 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