Align L-lysine transport protein (characterized)
to candidate SMa1668 SMa1668 ArcD2 arginine/ornithine antiporter
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__Smeli:SMa1668 Length = 473 Score = 371 bits (953), Expect = e-107 Identities = 199/487 (40%), Positives = 295/487 (60%), Gaps = 17/487 (3%) Query: 17 SRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLA 76 ++ +S+ L +++GS VGAGIFS+P+ G GP +I W IAG GM +A VF LA Sbjct: 2 AQKLSLFALTGMVVGSMVGAGIFSLPRTFGVATGPFGAIIAWCIAGGGMYMLARVFQSLA 61 Query: 77 RRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDH 136 RKP LD+GV+AYA+ G GDY GF SA+GYW+GS I V Y L STLG++ P+F + Sbjct: 62 ERKPDLDAGVFAYAKEGFGDYPGFLSAFGYWIGSCIGNVSYWVLIKSTLGNFFPVFGDGN 121 Query: 137 PFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTV 196 V+ L S WL ++ RGI QAAF+ TV TVAK++P++ FII++ F F + F + Sbjct: 122 TVVAILFASVGIWLFHFMILRGIQQAAFVNTVVTVAKVIPIIAFIIILFFF-FKLDLFRL 180 Query: 197 DLWARDG-GVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLL 255 + W +G ++ Q++ M+ TV+VFIGIEGAS YSR A++RSD+ AT++GF+ V Sbjct: 181 NFWGGEGMPEATLLQQIQATMLATVFVFIGIEGASNYSRYAQARSDIGTATIMGFIGVSA 240 Query: 256 LLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQML 315 L+V ++ L + LT+ E+AA+ SMA VL AVVGPWGA IS+G+ +SVLGAY++W ++ Sbjct: 241 LMVLVTLLPYAALTRPEIAAMSQPSMAGVLAAVVGPWGAVFISIGVIVSVLGAYLAWSLV 300 Query: 316 CAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLAT 375 CAE L + A +P G N A ++ IV+Q+F+I + ++ + M+ L + Sbjct: 301 CAEVLYVAARTDDMPRLFGTENQNKVPAAALWLTNIVVQLFVISTYWSQDAFALMLNLTS 360 Query: 376 NLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSV 435 ++ L+PY+F A + MLA R + E+ RE + LI+ +A VY+ Sbjct: 361 SMSLIPYMFVAAFGFMLAQRAETY--------------EVRPRERTRDLIIASIAAVYTF 406 Query: 436 WLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFN-RFEIGVVVVLVVAASAGVIGL 494 ++ A +FVL A+ PG I Y W R RG++VFN + + V+ A +IGL Sbjct: 407 FMIVAGGIKFVLLSALLYAPGTILYFWARRERGKRVFNTSIDWLIFATAVIGCFAAIIGL 466 Query: 495 VNGSLSL 501 G L++ Sbjct: 467 STGYLTI 473 Lambda K H 0.327 0.139 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: 676 Number of extensions: 43 Number of successful extensions: 3 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: 501 Length of database: 473 Length adjustment: 34 Effective length of query: 467 Effective length of database: 439 Effective search space: 205013 Effective search space used: 205013 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