Align high affinity cationic amino acid transporter 1 (characterized)
to candidate H281DRAFT_02180 H281DRAFT_02180 amino acid/polyamine/organocation transporter, APC superfamily
Query= CharProtDB::CH_091324 (622 letters) >FitnessBrowser__Burk376:H281DRAFT_02180 Length = 463 Score = 252 bits (644), Expect = 2e-71 Identities = 156/428 (36%), Positives = 240/428 (56%), Gaps = 34/428 (7%) Query: 13 MLRRKVVD----CSREESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVI 68 + R+K V+ S + + L + L DL LGVG+ +G G++VL G A + AGPA+++ Sbjct: 3 LFRKKSVEHMIATSAQNAGLKKALGALDLTFLGVGAIIGTGIFVLTGTGAVQ-AGPALMV 61 Query: 69 SFLIAALASVLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSV 128 SFLIAA+A A L Y EF + +P GS Y YSY T+GEL A+I GW+L+L Y + TS+V Sbjct: 62 SFLIAAVACGFAALAYAEFASTIPVAGSIYTYSYATLGELAAWIIGWDLMLEYGLATSAV 121 Query: 129 ARAWSATFDELIGKPIGEFSRQHMALN-APGVLAQTPDIF---AVIIIIILTGLLTLGVK 184 + WS L+ G +AL APG L +F A ++++ +T LL++GV+ Sbjct: 122 SVGWSGYLQSLLS---GFGVSLPVALTAAPGALPGHETLFNLPAFLVMMAITALLSVGVR 178 Query: 185 ESAMVNKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFG 244 ESA +N I I V+V+ ++ G + NW FMP G Sbjct: 179 ESARINNIMVAIKVVVVLLVIAVGVFHVTPANWH--------------------PFMPNG 218 Query: 245 FSGVLSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLM 304 ++GV AA F+AF+GFD +++ EEVKNP++ +P+GI+ASL +C + Y V+A +T + Sbjct: 219 WNGVFGAAAVMFFAFIGFDSVSSAAEEVKNPKRDLPIGIIASLGVCAVLYVAVAAVVTGI 278 Query: 305 MPYF-CLDIDSPLPGAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGL 363 +P +I P+ A + G + + +G++ + T +L + RVI+AM+ DGL Sbjct: 279 VPSAQFANISHPVSYALQVAGQKWVAGFIDLGAVLGMLTVILVMAYGQTRVIFAMSRDGL 338 Query: 364 LFKFLAKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVL 423 L L++++ R TP T G ++ L L L +L++IGTL A+S+V+ VLVL Sbjct: 339 LPARLSRVHPRFATPFFTTWLVGIFFGLIGALVPLNVLAELINIGTLAAFSMVSIAVLVL 398 Query: 424 R-YQPEQP 430 R PE P Sbjct: 399 RKTHPELP 406 Score = 64.7 bits (156), Expect = 8e-15 Identities = 47/140 (33%), Positives = 71/140 (50%), Gaps = 19/140 (13%) Query: 457 SQTGFLPVAEKFSLKSILSPKNVEPSKFSGLIVNISAGLLAALIITVCIVAVLGREALAE 516 S+ G LP S + P+ P F+ +V I GL+ AL+ + E + Sbjct: 334 SRDGLLPAR-----LSRVHPRFATPF-FTTWLVGIFFGLIGALVPLNVLA-----ELINI 382 Query: 517 GTLWAVFVMTGSVLLCMLVTGIIWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQ 576 GTL A +++ +VL + R+ + +F+ P VPV+PVL++ ++LM L Sbjct: 383 GTLAAFSMVSIAVL--------VLRKTHPELPRAFRCPGVPVVPVLAVASCVFLMANLQA 434 Query: 577 GTWVRFAVWMLIGFTIYFGY 596 TWV F VW+LIG IYFGY Sbjct: 435 VTWVAFVVWLLIGMVIYFGY 454 Lambda K H 0.324 0.138 0.417 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: 714 Number of extensions: 37 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 622 Length of database: 463 Length adjustment: 35 Effective length of query: 587 Effective length of database: 428 Effective search space: 251236 Effective search space used: 251236 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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