Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate N515DRAFT_1367 N515DRAFT_1367 Predicted arabinose efflux permease, MFS family
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Dyella79:N515DRAFT_1367 Length = 437 Score = 172 bits (437), Expect = 2e-47 Identities = 127/420 (30%), Positives = 202/420 (48%), Gaps = 52/420 (12%) Query: 2 MQTSSPPTPKGIWKVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWL-- 59 + +S+P + + + ++ G +E+YDF +F L F+ P WL Sbjct: 11 LDSSAPRLNRNDLRTLALAALGGALEFYDFVVFVFFTKALGQLFFPADMP-----EWLAQ 65 Query: 60 ----GTFAVGFLVRPFGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAW 115 G FA G+L RP G IV GD GRK + +++ +M T IGLLPT LG + Sbjct: 66 VQVYGIFAAGYLARPLGGIVMAHFGDRTGRKRMFTLSVFLMALPTLCIGLLPTYAQLGVF 125 Query: 116 AGIILITMRILQGLALGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILI 175 A ++L+ +R++QG+A+GG+ GA FVAEHAP G+ GF + + + T G+LI ++ Sbjct: 126 APMLLLLLRVVQGVAIGGEVPGAWVFVAEHAPPGRVGFACASLTSGLTAGILIG-SLVAA 184 Query: 176 TRISLGEADFNEWGWRLPFMASILLVILSLWIRRALKESPLFQQLKDTKAV-SKNPLKES 234 +G +GWRLPF+ + ++W+RR L E+P+F +L++ K + S+ PLK Sbjct: 185 GVTGMGAEKMLAYGWRLPFILGGVFGFFAVWLRRWLSETPVFAELRERKELASELPLKRV 244 Query: 235 FANPYNLRWVLIALFGATMGQGVVWYTGQFYALFYL------QKIFNTP---LIDSNLIV 285 +L VL+++ V W + L Q F+ P N + Sbjct: 245 MTG--HLGGVLLSML-------VTWMLTAAVVVVILMTPTLVQSSFHLPQKLAFHGNSL- 294 Query: 286 GAALLLSMPFFVFFGSLSDRIGRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFA 345 AAL+L + G DR GR +L G + ++T Y +Y + A +HF+ Sbjct: 295 -AALMLCFG-CIAGGVAVDRFGRGWSLLVGSVALLVTTYLLYRDLGQGA-----EHFMLL 347 Query: 346 YIGYNPVILGLLVFIQVIYVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVP 405 Y + GL V V G + A +V FP +R++ +S Y+I VFG + P Sbjct: 348 Y-----ALAGLCV--------GVVGVVPAVMVAAFPPAVRFSGLSFSYNIAYAVFGAITP 394 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: 603 Number of extensions: 51 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: 437 Length adjustment: 33 Effective length of query: 435 Effective length of database: 404 Effective search space: 175740 Effective search space used: 175740 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