Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate BPHYT_RS28490 BPHYT_RS28490 MFS transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__BFirm:BPHYT_RS28490 Length = 461 Score = 251 bits (640), Expect = 5e-71 Identities = 159/440 (36%), 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++ RPFGA Sbjct: 21 RVLAASVVGTAIEWYDFFLYATASALVFAKLFFPSFDPVVGTIAAFGSFAVGYVARPFGA 80 Query: 74 IVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGG 133 + FG GD +GRK T + T+TIMG TF+IGLLPT +G WA I+L+ MR +QGL +GG Sbjct: 81 VFFGHFGDRIGRKATLVATLTIMGVSTFVIGLLPTYASIGVWAPILLVAMRFMQGLGVGG 140 Query: 134 QYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLP 193 ++GGA V E AP KRGF+ ++ Q GL++S V S+ F WGWRLP Sbjct: 141 EWGGAVLMVVETAPARKRGFFGAFPQLGVPLGLMLSTAVFKAVS-SMPSDAFYSWGWRLP 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 FLLSVALIAIGLFIRLRVMESPVFEQIKASKQVVKAPLVELLRRHPKD----LVLTIGTR 255 Query: 253 MGQGVVWYTGQFYALFY--LQKIFNTPLIDSNLIVGAAL-LLSMPFFVFFGSLSDRIGRK 309 + + + L Y + + L+ + +IVG A L+++P FG LSD IGR+ Sbjct: 256 FAVDITFNVINVFVLVYGTTRLGLSRGLLLNAIIVGCAFALITLP---LFGKLSDVIGRR 312 Query: 310 KVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVY 369 V + G + + + + L+ PT ++ Y + G+ + VY Sbjct: 313 TVFMLGAVFVAIYGFAFFPLLETRNPT-------LIFVAY---VCGI-----ALSQASVY 357 Query: 370 GPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIA 429 G + + ELF T++RYT SLPY I + G P+I L G + A Sbjct: 358 GVQSTWFAELFGTRVRYTGASLPYQIAGIITSGPTPLIATYLFATYGQTLPISIYIAATG 417 Query: 430 GICLVVGFLLIKETNKVDIS 449 + LV F L ET + D+S Sbjct: 418 LLSLVCAFFL-AETFRRDLS 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: 682 Number of extensions: 48 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: 461 Length adjustment: 33 Effective length of query: 435 Effective length of database: 428 Effective search space: 186180 Effective search space used: 186180 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