Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate N515DRAFT_0011 N515DRAFT_0011 MFS transporter, MHS family, alpha-ketoglutarate permease
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Dyella79:N515DRAFT_0011 Length = 435 Score = 207 bits (528), Expect = 4e-58 Identities = 129/430 (30%), Positives = 218/430 (50%), Gaps = 26/430 (6%) Query: 17 IFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAIVF 76 IF+ S G ++EWYD+Y++ A + A F+ ++ G FAVGFL+RP G + Sbjct: 24 IFSGSIGNLVEWYDWYVYSAFSLYFAQVFFPASDQTTQLLNTSGIFAVGFLMRPLGGWLL 83 Query: 77 GRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQYG 136 G D GRK L+++ +M + +IGL P +G A I+L+ R+LQGL++GG+YG Sbjct: 84 GTFADRRGRKAALLLSVFMMSLGSLIIGLSPGYAQIGVAAPILLVLARLLQGLSIGGEYG 143 Query: 137 GAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITR-ISLGEADFNEWGWRLPFM 195 +AT+++E AP+ RGF++S T G LI+L ++++ + L ++WGWR+PF+ Sbjct: 144 TSATYLSEMAPRESRGFWSSIQYVTLVAGQLIALALLVVLQHFVLSTQQLHDWGWRIPFL 203 Query: 196 ASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATMGQ 255 LL ++++ IRR + E+ F++ + ++PL+ +P ++ + G TMG Sbjct: 204 IGALLAVIAVIIRRNMDETASFKKARQL----ESPLRTLMRHPRE----VLTVIGLTMGG 255 Query: 256 GVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDRIGRKKVMLSG 315 + +YT Y +L D+ I AAL + FG+LSDRIGR+ +++ Sbjct: 256 TLAFYTFTTYMQKFLVNSAGMSKADATSISTAALFVYALLQPAFGALSDRIGRRPLLIGF 315 Query: 316 MLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVYGPIAAF 375 +L L YPI + H + G L+ +I V+ A Sbjct: 316 GVLGALLTYPILSTLKE-------AHDWWQAFG--------LIMAALIIVSGYTSINAVV 360 Query: 376 LVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIAGICLVV 435 ELFPT+IR + LPY + VFGG + L D+ +W + C ++ Sbjct: 361 KAELFPTEIRAIGVGLPYALALSVFGGTAEYVALWFKKIGHEDY--FYWYVTACIACSLL 418 Query: 436 GFLLIKETNK 445 ++ +++T + Sbjct: 419 VYIGMRDTRR 428 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: 602 Number of extensions: 36 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: 435 Length adjustment: 33 Effective length of query: 435 Effective length of database: 402 Effective search space: 174870 Effective search space used: 174870 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