Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate HSERO_RS16820 HSERO_RS16820 alpha-ketoglutarate permease
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__HerbieS:HSERO_RS16820 Length = 465 Score = 214 bits (546), Expect = 4e-60 Identities = 136/439 (30%), Positives = 227/439 (51%), Gaps = 32/439 (7%) Query: 3 QTSSPPTPKGIWKVIFA---SSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWL 59 Q S+P + K IFA +S+G ++EW+DFY++ A A F+ G P ++ Sbjct: 14 QASTPLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQLLNTA 73 Query: 60 GTFAVGFLVRPFGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGII 119 G FA GFL+RP G +FGRI D GRK + LI++ +M + + ++PT +GAWA + Sbjct: 74 GVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGAWAPAL 133 Query: 120 LITMRILQGLALGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRIS 179 L+ R+ QGL++GG+YG +AT+++E AP G+RGF+ S+ T G L+++ V+ + Sbjct: 134 LLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLFGMQQW 193 Query: 180 LGEADFNEWGWRLPFMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPL---KESFA 236 L +A+ WGWR+PF+ + ++++++R +L E+ K A + L K +F Sbjct: 194 LTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQHKRAFL 253 Query: 237 NPYNLRWVLIALFGATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFF 296 N + G T G +++YT Y YL +N ++ AL + M Sbjct: 254 N----------VVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQ 303 Query: 297 VFFGSLSDRIGRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGL 356 FG++SD+IGR+ ML ++ +PI + + PG + L + Sbjct: 304 PIFGAISDKIGRRNSMLCFAFFGMVGTFPILHFLKDV--SSPGV----------AMALAI 351 Query: 357 LVFIQVIYVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATG 416 L V + T + G I A E+FP ++R + L Y +GN +FGG + L L +A G Sbjct: 352 LALTIVSFYTSISGLIKA---EMFPPEVRALGVGLSYAVGNAIFGGSAEFVALSLKSA-G 407 Query: 417 NDFAGLWWPMAIAGICLVV 435 + A W+ A+ + L++ Sbjct: 408 IESAFYWYVSALCLVALII 426 Lambda K H 0.328 0.144 0.450 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: 632 Number of extensions: 37 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: 468 Length of database: 465 Length adjustment: 33 Effective length of query: 435 Effective length of database: 432 Effective search space: 187920 Effective search space used: 187920 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: 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