Align Amino acid transporter (characterized, see rationale)
to candidate N515DRAFT_2925 N515DRAFT_2925 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= uniprot:A0A0H3C3Q5 (483 letters) >FitnessBrowser__Dyella79:N515DRAFT_2925 Length = 480 Score = 312 bits (799), Expect = 2e-89 Identities = 176/460 (38%), Positives = 267/460 (58%), Gaps = 19/460 (4%) Query: 30 LKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGL-AGPGVILSFLIAGAVCACAALCYAEL 88 L++TL + ALG+GA++GTGI+ +TG A AGP V++SF++A ALCYAE Sbjct: 24 LRRTLGKWGITALGIGAVIGTGIFVVTGQAAAEHAGPAVLISFMLAAICSGFTALCYAEF 83 Query: 89 STMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVGWSAHAHGLFKMIGF-- 146 +T+IP SGS+Y+Y+YA +GE VAWF+GW+++LEY + +AVA W+ + L +G Sbjct: 84 ATLIPISGSSYSYAYATLGELVAWFIGWNMVLEYGISASAVAASWTGYFTSLLDHVGIHL 143 Query: 147 PDALLAGP---------HQGGLINMPAVFISMAVAGLLALGTRESATVNMVLVFVKIIAL 197 P AL P G L+N+PAV I +A+ L +G RES+ +N+++V +K+ + Sbjct: 144 PVALTEAPLAFKDGHLVTTGHLLNLPAVAIVLALTWLCYVGIRESSGLNVLMVALKVGLI 203 Query: 198 IVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGVMAAASLIFFAFYGFDAVST 257 IV VV + A++ PF+P E G+M A+++FFA+ GF+A ST Sbjct: 204 IVVVVAGYRYVDPANWHPFIP-------AEQEPGKYGWSGIMRGAAMVFFAYIGFEATST 256 Query: 258 AAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPLVFILESLNHG 317 AA+E KNP++DL G + S+ +CT +Y+ +AAV G SE + I G Sbjct: 257 AAQECKNPQKDLPFGTLVSLVICTVLYLAMAAVLTGLIPYTELGTSEPVVTAIRNHPELG 316 Query: 318 KIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGTPVMMTLLTG 377 + +V + A+I L +VIL + Q RIF +M+RDGLLP ++++ K TP + T++TG Sbjct: 317 WLRLVVEIGAMIGLSSVILVMIIAQPRIFMIMSRDGLLPPVFNRIHPKHRTPHLNTVITG 376 Query: 378 VLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFSTPLWPIVAPAG 437 + A+++ + L +A+L + GTL AF+AV A V++LR P PR+F P V AG Sbjct: 377 IGIAILAAVFPLDLLADLTSMGTLIAFVAVCAGVLILRYTAPELPRLFRVPAAWFVCTAG 436 Query: 438 ILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVL 477 + CL L + L + IG +Y YGMR S L Sbjct: 437 VFSCLALLYFMAWFNWLLMIIWTAIGLAIYFGYGMRHSRL 476 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: 643 Number of extensions: 36 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: 480 Length adjustment: 34 Effective length of query: 449 Effective length of database: 446 Effective search space: 200254 Effective search space used: 200254 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