Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate H281DRAFT_02516 H281DRAFT_02516 Nitrate/nitrite transporter NarK
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Burk376:H281DRAFT_02516 Length = 457 Score = 314 bits (805), Expect = 3e-90 Identities = 161/438 (36%), Positives = 261/438 (59%), Gaps = 13/438 (2%) Query: 1 MMQTSSPPTPK-GIWKVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWL 59 M TS P+ G+ ++I SS GT++E+YDF+++ AL +TL F + + +A + Sbjct: 1 MSTTSGARDPQPGMLRIIATSSIGTMLEYYDFFVYVALTSTLTHLFLPSTDRMIATMAGV 60 Query: 60 GTFAVGFLVRPFGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGII 119 TF + ++ RP G I+F + D +GRK T++IT+ IMG T IG LPT + G A I Sbjct: 61 ATFGIAYVARPLGTIIFSPMADRIGRKKTFVITLAIMGIATVGIGCLPTYAMAGLLAPIG 120 Query: 120 LITMRILQGLALGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRIS 179 L+T+R++QG+ALGG+YG A +V EHAP G++G TS +Q+TA+ GLL++L ++ + + Sbjct: 121 LVTLRVVQGIALGGEYGSAVVYVMEHAPAGRKGMATSVLQSTASLGLLLALAIVSALKFA 180 Query: 180 LGEADFNEWGWRLPFMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPY 239 L + F WGWR+PF+ S +V ++ WIR + E+P+F ++K +SK+PL+++ ++ Sbjct: 181 LDASAFESWGWRVPFLISAPIVAVATWIRLGMTETPVFAEMKQAGRLSKSPLQDTLSSAT 240 Query: 240 NLRWVLIALFGATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFF 299 + + +L+A+FGA G V YT Y L++LQ + +NL +G A++++ P + F Sbjct: 241 SWKAILVAMFGAQGGTSVSLYTSIVYMLYFLQNVLKVEPSRANLCLGIAIVVAAPLYPVF 300 Query: 300 GSLSDRIGRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVF 359 G LSD IGR +VML G++L +L YP + + A + ++ LLV Sbjct: 301 GRLSDAIGRSRVMLIGIVLWILAAYPAFAGIRTNA------------LAGGWAMVTLLVA 348 Query: 360 IQVIYVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDF 419 + + M+ P+ AF+ E FP + R T L +GN +FGG +P+I L L+N TGN Sbjct: 349 LLAVLTAMIMAPLPAFIAECFPPQSRTTGFGLSQQLGNVLFGGFLPLISLSLVNLTGNPL 408 Query: 420 AGLWWPMAIAGICLVVGF 437 AG+ + + CL V + Sbjct: 409 AGVGYSIVSLLPCLAVTY 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: 607 Number of extensions: 43 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: 457 Length adjustment: 33 Effective length of query: 435 Effective length of database: 424 Effective search space: 184440 Effective search space used: 184440 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