Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate AO353_17220 AO353_17220 alpha-ketoglutarate permease
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__pseudo3_N2E3:AO353_17220 Length = 431 Score = 223 bits (567), Expect = 1e-62 Identities = 135/432 (31%), Positives = 230/432 (53%), Gaps = 23/432 (5%) Query: 11 KGIWKVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRP 70 K I+ ++ ASS G ++EW+DFY++ A A F+ + P ++ G FA GFL+RP Sbjct: 15 KRIFAIVGASS-GNLVEWFDFYVYAFCAIYFAPAFFPSDNPTVQLVNTAGVFAAGFLMRP 73 Query: 71 FGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLA 130 G +FGR+ D GRK + +I++ +M + + LI LPT +G WA ++L+ R++QG++ Sbjct: 74 IGGWLFGRVADKHGRKNSMMISVLMMCAGSLLIACLPTYKDIGVWAPLLLLVARLIQGVS 133 Query: 131 LGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGW 190 +GG+YG AT+++E A +G+RGF+ S+ T G L+++ +++I + L E D WGW Sbjct: 134 VGGEYGTTATYMSEVALKGQRGFFASFQYVTLIGGQLLAVSLVVILQQFLTEDDLRAWGW 193 Query: 191 RLPFMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFG 250 R+PF+ ++SL++RR+LKE+ + ++ A S L N I + G Sbjct: 194 RIPFVVGAAAALISLFLRRSLKETTSKEMRENKDAGSMAALFR------NNTAAFITVLG 247 Query: 251 ATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDRIGRKK 310 T G +++YT Y YL P ++ I+ AL L M FG+L+D+IGR+ Sbjct: 248 FTAGGSLIFYTFTTYMQKYLVNTAGMPAKTASYIMTGALFLYMCMQPLFGTLADKIGRRN 307 Query: 311 VMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVYG 370 ML L L PI L+ + T+P ++ + + + L + V + T + G Sbjct: 308 SMLWFGALGTLFTVPI--LLTLKSVTNP-------FLAFGLITVALAI---VSFYTSISG 355 Query: 371 PIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIAG 430 + A E+FP ++R + L Y + N +FGG + L L + G + + W+ A+ Sbjct: 356 LVKA---EMFPPQVRALGVGLAYAVANAIFGGSAEYVALSL-KSVGIENSFYWYVTAMMA 411 Query: 431 ICLVVGFLLIKE 442 I + L ++ Sbjct: 412 IAFLFSLRLPRQ 423 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: 610 Number of extensions: 28 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: 431 Length adjustment: 33 Effective length of query: 435 Effective length of database: 398 Effective search space: 173130 Effective search space used: 173130 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