Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate AO356_22475 AO356_22475 MFS transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_22475 Length = 447 Score = 236 bits (601), Expect = 2e-66 Identities = 142/445 (31%), Positives = 238/445 (53%), Gaps = 25/445 (5%) Query: 11 KGIWKVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIG-DIIAWLGTFAVGFLVR 69 K + V+ S GT +E YD Y++G A + + + GT +A L +FA+ F+ R Sbjct: 22 KSMKNVVAGSLFGTALETYDLYLYGTAAALIFAPLFFPGTDEAVSRLASLASFAISFVAR 81 Query: 70 PFGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGL 129 P G++V G GD +GRK +T+ IMG T IGLLPT +G WA I+L +R +QG Sbjct: 82 PLGSLVLGHFGDRIGRKKLLYLTLIIMGLSTVGIGLLPTYASVGIWAPIMLCVLRFIQGF 141 Query: 130 ALGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWG 189 A G+Y GA + EHAP+ KRGFY + FG + S G++LI L DF +WG Sbjct: 142 AFAGEYSGAVLMLLEHAPRRKRGFYAAINNIGPVFGFIASAGLLLIVSSLLSVEDFYKWG 201 Query: 190 WRLPFMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNP-LKESFANPYNLRWVLIAL 248 WR+PF+AS+ L+++ +++R + ESP+F++ + +A +K P L + L+ + Sbjct: 202 WRIPFIASLALLVVGVFVRSKVAESPVFEKTAEKRAAAKGPNLSPAMRLFTKYPKQLLLV 261 Query: 249 FGATMGQGVVWYTGQFYALFYLQK---IFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDR 305 GA + +Y +AL Y QK + N ++ ++ L+ +P F G+++DR Sbjct: 262 AGANICHFSTFYLFTVFALSYGQKELGLSNAFVLSVAMVAICTHLVIVP---FAGAMADR 318 Query: 306 IGRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYV 365 +GR+ +ML G ++ L +P + L + GQ + P++LG +F + Sbjct: 319 LGRRTMMLIGFVVTALAAFPFWHLFST------GQ--------FLPMVLGSCLF--MAGY 362 Query: 366 TMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWP 425 +VYG + +F E F R+T ++ ++G + GG P++G L++ G+ +A + Sbjct: 363 GLVYGAVPSFTGEAFGPSARFTGFAMATNVGGIIGGGTAPIVGAYLLSHYGSPYAISVYT 422 Query: 426 MAIAGICLVVGFLLIKETNKVDISD 450 + +A I + + L ET +DI+D Sbjct: 423 VVLAAISALCVY-LSAETRMIDITD 446 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: 612 Number of extensions: 44 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: 468 Length of database: 447 Length adjustment: 33 Effective length of query: 435 Effective length of database: 414 Effective search space: 180090 Effective search space used: 180090 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