Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate H281DRAFT_02948 H281DRAFT_02948 metabolite-proton symporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Burk376:H281DRAFT_02948 Length = 460 Score = 257 bits (656), Expect = 7e-73 Identities = 163/440 (37%), Positives = 234/440 (53%), Gaps = 29/440 (6%) Query: 15 KVIFASSAGTVIEWYDFYIFG-ALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGA 73 +V+ AS GT IEWYDF+++ A A A F+ + P+ IA G+FAVG+L RPFGA Sbjct: 21 RVLVASVVGTAIEWYDFFLYATASALVFAKLFFPSFDPVVGTIAAFGSFAVGYLARPFGA 80 Query: 74 IVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGG 133 + FG GD +GRK T + T+TIMG TF+IGLLPT D +G WA I+L+ MR LQGL +GG Sbjct: 81 VFFGHFGDRIGRKTTLVATLTIMGVGTFVIGLLPTYDSIGVWAPILLVAMRFLQGLGVGG 140 Query: 134 QYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLP 193 ++GGA V E AP KRGF+ ++ Q GL++S V SL F WGWRLP Sbjct: 141 EWGGAVLMVVETAPASKRGFFGAFPQLGVPLGLMLSTAVFKAVS-SLPSDAFYSWGWRLP 199 Query: 194 FMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESF-ANPYNLRWVLIALFGAT 252 F+ S+ L+ + L+IR + ESP+F+Q+K +K V K PL E +P + L+ G Sbjct: 200 FLLSVALIAIGLFIRLRVMESPVFEQIKASKQVVKAPLIELLRRHPKD----LVLTIGTR 255 Query: 253 MGQGVVWYTGQFYALFYLQKIFNTP--LIDSNLIVGAAL-LLSMPFFVFFGSLSDRIGRK 309 + + + L Y P L+ + +I+G A L+++P FG LSD IGR+ Sbjct: 256 FAVDITFNVINVFVLVYGTTRLGLPRGLLLNAIILGCAFALITLP---LFGKLSDLIGRR 312 Query: 310 KVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVY 369 V + G + + + + L+ PT +IL V + VY Sbjct: 313 TVFMFGAVFVAIYGFAFFPLLETRNPT---------------LILVAYVCGIALSQASVY 357 Query: 370 GPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIA 429 G + + ELF T++RYT SLPY I + G P+I L AT + +A Sbjct: 358 GVQSTWFAELFGTRVRYTGASLPYQIAGIITSGPTPLIATYLF-ATYGQTLPISIYIAAT 416 Query: 430 GICLVVGFLLIKETNKVDIS 449 G+ +V + ET + D+S Sbjct: 417 GLLSMVCAFFLAETFRRDLS 436 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: 698 Number of extensions: 45 Number of successful extensions: 7 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: 460 Length adjustment: 33 Effective length of query: 435 Effective length of database: 427 Effective search space: 185745 Effective search space used: 185745 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