Align high affinity cationic amino acid transporter 1 (characterized)
to candidate N515DRAFT_2925 N515DRAFT_2925 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= CharProtDB::CH_091324 (622 letters) >FitnessBrowser__Dyella79:N515DRAFT_2925 Length = 480 Score = 261 bits (667), Expect = 5e-74 Identities = 153/439 (34%), Positives = 240/439 (54%), Gaps = 58/439 (13%) Query: 20 DCSREESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVL 79 DC S L R L + + ALG+G+ +G G++V+ G A E+AGPA++ISF++AA+ S Sbjct: 17 DCHGGPS-LRRTLGKWGITALGIGAVIGTGIFVVTGQAAAEHAGPAVLISFMLAAICSGF 75 Query: 80 AGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDEL 139 LCY EF +P +GS+Y Y+Y T+GEL A+ GWN++L Y I S+VA +W+ F L Sbjct: 76 TALCYAEFATLIPISGSSYSYAYATLGELVAWFIGWNMVLEYGISASAVAASWTGYFTSL 135 Query: 140 IGKPIGEFSRQHMALNAPGVLAQTPDIF---------------AVIIIIILTGLLTLGVK 184 + H+ ++ P L + P F AV I++ LT L +G++ Sbjct: 136 L---------DHVGIHLPVALTEAPLAFKDGHLVTTGHLLNLPAVAIVLALTWLCYVGIR 186 Query: 185 ESAMVNKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMP-- 242 ES+ +N + + V ++ +VV+G+ NW F+P Sbjct: 187 ESSGLNVLMVALKVGLIIVVVVAGYRYVDPANWH--------------------PFIPAE 226 Query: 243 -----FGFSGVLSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGV 297 +G+SG++ GAA F+A++GF+ +T +E KNPQK +P G + SL+IC + Y + Sbjct: 227 QEPGKYGWSGIMRGAAMVFFAYIGFEATSTAAQECKNPQKDLPFGTLVSLVICTVLYLAM 286 Query: 298 SAALTLMMPYFCLDIDSPLPGAFKHQ---GWEEAKYAVAIGSLCALSTSLLGSMFPMPRV 354 +A LT ++PY L P+ A ++ GW + V IG++ LS+ +L + PR+ Sbjct: 287 AAVLTGLIPYTELGTSEPVVTAIRNHPELGW--LRLVVEIGAMIGLSSVILVMIIAQPRI 344 Query: 355 IYAMAEDGLLFKFLAKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYS 414 M+ DGLL +I+ + +TP + TV +G A++A +F L L DL S+GTL+A+ Sbjct: 345 FMIMSRDGLLPPVFNRIHPKHRTPHLNTVITGIGIAILAAVFPLDLLADLTSMGTLIAFV 404 Query: 415 LVAACVLVLRY-QPEQPNL 432 V A VL+LRY PE P L Sbjct: 405 AVCAGVLILRYTAPELPRL 423 Score = 40.4 bits (93), Expect = 2e-07 Identities = 39/131 (29%), Positives = 57/131 (43%), Gaps = 20/131 (15%) Query: 474 LSPKNVEPSKFSGLIVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCM 533 + PK+ P + +I I +LAA + + ++A L + GTL A + VL Sbjct: 361 IHPKHRTPH-LNTVITGIGIAILAA-VFPLDLLADL----TSMGTLIAFVAVCAGVL--- 411 Query: 534 LVTGIIWRQPESKTKLSFKVP---FVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGF 590 I R + F+VP FV V S +Y M + W+ +W IG Sbjct: 412 -----ILRYTAPELPRLFRVPAAWFVCTAGVFSCLALLYFMAWFN---WLLMIIWTAIGL 463 Query: 591 TIYFGYGIWHS 601 IYFGYG+ HS Sbjct: 464 AIYFGYGMRHS 474 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: 743 Number of extensions: 31 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 622 Length of database: 480 Length adjustment: 36 Effective length of query: 586 Effective length of database: 444 Effective search space: 260184 Effective search space used: 260184 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