Align Osmoregulated proline transporter OpuE; Osmoprotectant uptake; Proline uptake system (characterized)
to candidate 6936303 Sama_0492 sodium/proline symporter (RefSeq)
Query= SwissProt::O06493 (492 letters) >FitnessBrowser__SB2B:6936303 Length = 498 Score = 557 bits (1435), Expect = e-163 Identities = 278/496 (56%), Positives = 368/496 (74%), Gaps = 6/496 (1%) Query: 1 MSIEIIISLGIYFIAMLLIGWYAFKKTTD-INDYMLGGRGLGPFVTALSAGAADMSGWML 59 M ISL +YFIAML IG +A++ +TD + YMLGGR + P VTALSAGA+DMSGWML Sbjct: 1 MEYSSYISLALYFIAMLAIGLFAYRNSTDDLAGYMLGGRQVSPHVTALSAGASDMSGWML 60 Query: 60 MGVPGAMFATGLSTLWLALGLTIGAYSNYLLLAPRLRAYTEAADDAITIPDFFDKRFQHS 119 MG+PGAMF G LW+A GL +GA NYLL+APRLR +TEAADDA+T+PDFF KRF Sbjct: 61 MGLPGAMFTMGYDALWIAAGLLLGALLNYLLVAPRLRVFTEAADDALTLPDFFSKRFNKD 120 Query: 120 SSLLKIVSALIIMIFFTLYTSSGMVSGGRLFESAFGADYKLGLFLTTAVVVLYTLFGGFL 179 + ++++SA +I++FFTLYTS+G+V+GG+ FESAFG Y+ GL LT +VVV YTL GGFL Sbjct: 121 NGSVRMISAAVIILFFTLYTSAGLVAGGKFFESAFGLGYQTGLLLTVSVVVAYTLLGGFL 180 Query: 180 AVSLTDFVQGAIMFAALVLVPIVAFTHVGGVAPTFHEIDAVNPHLLDIFKGASVISIISY 239 AVSLTDFVQG IMF ALVLVP+VA + L D F+ +++I+S Sbjct: 181 AVSLTDFVQGCIMFLALVLVPLVALQEFNSSTDMLAQASRSITPLADSFEHMGILAIVSS 240 Query: 240 LAWGLGYYGQPHIIVRFMAIKDIKDLKPARRIGMSWMIITVLGSVLTGLIGVAYAHKFGV 299 LAWGLGY+GQPHIIVRFMAI+ +KD+ AR IGMSWM++T+LG++ TGLIGVAY +KF Sbjct: 241 LAWGLGYFGQPHIIVRFMAIRSVKDIAVARNIGMSWMLVTILGALATGLIGVAYVNKFKP 300 Query: 300 AVKDPEMIFIIFSKILFHPLITGFLLSAILAAIMSSISSQLLVTASAVTEDLYRSFFRRK 359 + D E IFI+F++ILFHPLI+GFLL+AILAAIMS+ISSQLLV++S+++ED+YR+ F ++ Sbjct: 301 GLDDGETIFILFAEILFHPLISGFLLAAILAAIMSTISSQLLVSSSSLSEDVYRALFHKE 360 Query: 360 ASDKELVMIGRLSVLVIAVIAVLLSLNPNSTILDLVGYAWAGFGSAFGPAILLSLYWKRM 419 K V GR+ VL +A +A LL+L+ N++IL LV AWAGFG+AFGP +LLSL+W RM Sbjct: 361 MDQKATVTAGRIGVLAVAAVATLLALDNNASILSLVSNAWAGFGAAFGPLVLLSLFWPRM 420 Query: 420 NEWGALAAMIVGAATVLIW-----ITTGLAKSTGVYEIIPGFILSMIAGIIVSMITKRPA 474 GA+A ++ GA TVL+W + GL S+ +YEI+PGFI+S +A ++VS + P Sbjct: 421 THSGAVAGILCGAGTVLVWSQVPLLENGLPLSSLIYEIVPGFIVSTLAIVLVSYADQAPC 480 Query: 475 KASYRLFGVMEKLLKR 490 K++ + F + LK+ Sbjct: 481 KSTQKAFKLSRDRLKQ 496 Lambda K H 0.328 0.142 0.421 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: 38 Number of successful extensions: 5 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: 492 Length of database: 498 Length adjustment: 34 Effective length of query: 458 Effective length of database: 464 Effective search space: 212512 Effective search space used: 212512 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 (21.8 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