Align Cationic amino acid transporter 3 (characterized)
to candidate N515DRAFT_0722 N515DRAFT_0722 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= CharProtDB::CH_091036 (618 letters) >FitnessBrowser__Dyella79:N515DRAFT_0722 Length = 479 Score = 234 bits (597), Expect = 6e-66 Identities = 144/414 (34%), Positives = 223/414 (53%), Gaps = 35/414 (8%) Query: 28 LARCLSTLDLVALGVGSTLGAGVYVLAGEVAKDKAGPSIVICFLVAALSSVLAGLCYAEF 87 L R L +LV LGVG+ +GAG++V+ G+ A + AGP++ + F++A L++ LA L YAEF Sbjct: 23 LRRTLGLKELVVLGVGAVIGAGIFVITGQAAAEHAGPALTLSFVLAGLAAALAALSYAEF 82 Query: 88 GARVPGSGSAYLYSYVTVGELWAFTTGWNLILSYVIGTASVARAWSSAFDNL---IGNHI 144 A +P SGSAY+Y+Y T GEL A+ GWN++ Y++ +SVA WS L +G + Sbjct: 83 AAMLPVSGSAYVYAYATFGELLAWFIGWNVVAEYLLAVSSVAVGWSGYGVGLLKSLGIEV 142 Query: 145 SRTLKGTIL------LKMPHVLAEYPDFFALALVLLLTGLLVLGASKSALVTKVFTGMNL 198 L L L++ L P AL +V LT LL G +S + V + + Sbjct: 143 PAALANAPLSFKDGHLELTGALLNLP---ALLVVAALTALLYRGTRQSTMFASVVVALKV 199 Query: 199 LVLSFVIISGFIKGELRNWKLTKEDYCLTMSESNGTCSLDSMGSGGFMPFGLEGILRGAA 258 +V+ ++ G + W Y + G +G G+ R A Sbjct: 200 IVVVLFVVCGLQYVDPSLW----HPYV--------------PANQGGDHYGWAGVFRAAT 241 Query: 259 TCFYAFVGFDCIATTGEEAQNPQRSIPMGIVISMFICFLAYFGVSSALTLMMPYYKLHPE 318 + FYA++GFD +AT +E +NPQR++P GI+IS+ IC + Y V++ LT ++PY +L Sbjct: 242 SVFYAYIGFDAVATAAQETRNPQRNVPAGILISLAICTVLYIIVAAVLTGLVPYPQLATA 301 Query: 319 SPLPEAFSY---VGWEPARYLVAIGSLCALSTSLLGSMFPMPRVMYSMAEDGLLFRVLAK 375 P+ A + + W + L +G++ L++ +L + R++YSMA DGLL Sbjct: 302 EPVATALAAHPPLAW--LKLLTQVGAVAGLTSVILVMHLGLSRILYSMAGDGLLPTFFGA 359 Query: 376 VHSVTHIPIVATLVSGVIAAFMAFLFELTDLVDLMSIGTLLAHSLVSICVLILR 429 VH P TL+ G + +A +F L+ L DL+S+GTLLA + V I VL+LR Sbjct: 360 VHERHRTPHRTTLLVGAVGGVLAAVFPLSLLGDLLSMGTLLAFATVCIGVLVLR 413 Score = 53.9 bits (128), Expect = 2e-11 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 5/82 (6%) Query: 513 VLILGLILAISGV-----IWRQPQNRTPLHFKVPAVPLLPLVSIFVNVYLMMQMTAGTWA 567 +L +G +LA + V + R+ P F+VPA P + + + V +L+ QM G W Sbjct: 393 LLSMGTLLAFATVCIGVLVLRRTHPNLPRGFRVPAAPAVCTLGVLVCAFLLAQMNLGNWI 452 Query: 568 RFGIWMLIGFAIYFGYGIQHSM 589 W +G IY YG +HS+ Sbjct: 453 LLAAWTTLGMLIYIAYGYRHSL 474 Lambda K H 0.326 0.139 0.425 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: 662 Number of extensions: 37 Number of successful extensions: 4 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: 618 Length of database: 479 Length adjustment: 35 Effective length of query: 583 Effective length of database: 444 Effective search space: 258852 Effective search space used: 258852 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