Align L-lysine transport protein (characterized)
to candidate SMa1667 SMa1667 ArcD1 arginine/ornithine antiporter
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__Smeli:SMa1667 Length = 475 Score = 360 bits (924), Expect = e-104 Identities = 201/489 (41%), Positives = 291/489 (59%), Gaps = 18/489 (3%) Query: 15 ATSRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHV 74 +T++ +S+ +L AL++GS VGAGIFS+P+ G GP ++ W IAG G+ ++A VF V Sbjct: 3 STAQKLSLASLAALVVGSMVGAGIFSLPRTFGDATGPFGAIVAWCIAGAGIFTLAHVFRV 62 Query: 75 LARRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQ 134 LA RK LD+GVYAYA G GDY GF S GYWL IA V Y L +TLG + P+F Sbjct: 63 LAERKSDLDAGVYAYANAGFGDYAGFLSVLGYWLVGCIADVSYWVLIKATLGAFFPIFGD 122 Query: 135 DHPFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLG-FSWEK 193 + + L S W ++ RGI +AA + TV TVAKI+P+L FI+++ LG F + Sbjct: 123 GNTIAAVLVSSVALWGFHFMILRGIKEAAAINTVVTVAKIVPILIFIVIL--LGAFETDL 180 Query: 194 FTVDLWA-RDGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVA 252 F + W D S+F+Q+R M+ TV+VFIG+EGASVYSR AR RSDV AT +GFV Sbjct: 181 FRSNFWGGADMPEASLFEQIRATMLVTVFVFIGVEGASVYSRYARKRSDVGVATTLGFVV 240 Query: 253 VLLLLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSW 312 VL L+V ++ L +G L + E+AA+ SMASVLE++VGPWG+ +S GL +SVLGAY++W Sbjct: 241 VLGLMVLVTLLPYGALERPEIAAMRQPSMASVLESIVGPWGSVFVSAGLIVSVLGAYLAW 300 Query: 313 QMLCAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQ 372 ++C E L A +G +PS + NS A +S VIQ+F+I +E + MV Sbjct: 301 SLICVEVLFCAAKNGDMPSVLARENSNSVPAAALWLSNGVIQLFLISTLFSEDAFRLMVN 360 Query: 373 LATNLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATV 432 L + + L+PYL A Y ++A RG+ I +E + LI+ ATV Sbjct: 361 LTSAMVLIPYLLVAAYGFLVAKRGETY--------------NIRPKERFRDLILAGAATV 406 Query: 433 YSVWLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVI 492 Y+ ++ YA +F+L A+ G + + R + + +F+ E V + +V G+ Sbjct: 407 YTAFMIYAGGLKFLLLSAILYALGTALFFYARREQKKPLFSPREWLVFIAVVAGCLVGIY 466 Query: 493 GLVNGSLSL 501 GLV GS+++ Sbjct: 467 GLVTGSITI 475 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: 667 Number of extensions: 35 Number of successful extensions: 4 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: 475 Length adjustment: 34 Effective length of query: 467 Effective length of database: 441 Effective search space: 205947 Effective search space used: 205947 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