Align Alpha-ketoglutarate permease (characterized)
to candidate Pf6N2E2_1930 L-Proline/Glycine betaine transporter ProP
Query= SwissProt::P0AEX3 (432 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1930 Length = 456 Score = 209 bits (533), Expect = 1e-58 Identities = 141/424 (33%), Positives = 212/424 (50%), Gaps = 22/424 (5%) Query: 12 LTSSDTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAA 71 +T + T ++ + GN E +DF V+ F + FFP + T LL T V+A Sbjct: 1 MTKTKTTSSRRSLAAGAIGNFGEIYDFAVFGFSIPILSVHFFPGSDRTAALLSTFAVYAV 60 Query: 72 GFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLLLAR 131 F+ RP+GG +FG +AD+ GR + M ++V +M G+ +I LP Y TIG AP LLLL R Sbjct: 61 AFVARPLGGLMFGYLADRLGRIRVMAMTVWLMALGTAIIGLLPTYATIGIAAPLLLLLCR 120 Query: 132 LFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLV---VVVLQHTME 188 + QGL++GGE S +Y+ E A E R+G++ F TLI L +V VV LQ Sbjct: 121 IAQGLALGGETTGSTSYIVESAPENRRGYWLGF---TLIFSHLPNAVVAGLVVALQLGAG 177 Query: 189 DAALREWGWRIPFALGAVLAVVALWLRRQLDETSQ-QETRALKEAGSLK----------G 237 D A +W WRIPF LG ++ VV WLRR +DE + ++ R +A +K G Sbjct: 178 DQAYSDWAWRIPFLLGGIIGVVGFWLRRNIDEPEEYKQARQASKASKIKKNPLIAAIRCG 237 Query: 238 LWRNRRAFIMVLGFTAAGSLCFYTFTTYMQKYLVNTAGMHANVASGIMTAALFVFMLIQP 297 R MV + G+ Y +M +L+ + + A A+ V + P Sbjct: 238 GLRGMLHVFMVQPVFSVGA---YLLLGFMYTFLIEVGKLDSTSALISNAIAVIVLSALLP 294 Query: 298 LIGALSDKIGRRTSMLCFGSLAAIFTVPILSALQNVSSPYAAFGLVMCALLIVSFYTSIS 357 L G LSD+ GR+ + + A+ P + + S A G + A + Y + S Sbjct: 295 LGGLLSDRFGRKRVLTFGAAWIALSAYPAMYLAASGSFASAVAGQTLLAAGL-GIYGAAS 353 Query: 358 GILKAEMFPAQVRALGVGLSYAVANAIFGGSAEYVALSL-KSIGMETAFFWYVTLMAVVA 416 + AE FP RA G +SY + A+FGG+ +A L ++ G A +YVTL+AV+ Sbjct: 354 FVAAAEFFPTSFRATGHAISYQTSVAMFGGTCPLIAAYLSQAFGSPLAPAFYVTLIAVLC 413 Query: 417 FLVS 420 + + Sbjct: 414 LITT 417 Lambda K H 0.328 0.138 0.419 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: 527 Number of extensions: 27 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: 432 Length of database: 456 Length adjustment: 32 Effective length of query: 400 Effective length of database: 424 Effective search space: 169600 Effective search space used: 169600 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: 51 (24.3 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