Align Acetate uptake permease, ActP1; also takes up tellurite (characterized)
to candidate WP_086508553.1 BZY95_RS03245 cation acetate symporter
Query= TCDB::D5AU53 (551 letters) >NCBI__GCF_002151265.1:WP_086508553.1 Length = 598 Score = 150 bits (380), Expect = 1e-40 Identities = 88/281 (31%), Positives = 142/281 (50%), Gaps = 15/281 (5%) Query: 54 WAARRTKSTADFYTAGGGITGFQNGLAIAGDYMSAAAFLGISGMVFAKGVDGAIYTVGFT 113 WA R ST DFY AGGG+ NG+A A D+MSAA+F+ ++G++ + G + + +G+T Sbjct: 24 WA--RAGSTKDFYVAGGGVHPVTNGMATAADWMSAASFISMAGLLASGGYANSTFLMGWT 81 Query: 114 VGWPFILFLIAERLRNLGKFTFADITSFRLEQTRIRTLSALGALTVVVFYLIAQMVGAGK 173 G+ + L+A LR GKFT D R R ++ + + V Y+I QM GAG Sbjct: 82 GGYVILAMLLAPYLRKFGKFTVPDFIGDRFYSKTARVVAVICLIVASVTYVIGQMTGAGV 141 Query: 174 LIQLLFGLPYSYAVILVGVLMVLYVTFGGMLATTWVQIVKAVMLLSGATLLVILGLAQFG 233 +P S + + ++ LY FGGM T+ Q+ + ++L+ T+ + Q Sbjct: 142 AFSRFLEVPSSTGIWIAAGIVFLYAVFGGMKGITYTQVAQYIVLIIAYTIPAVFIAMQLT 201 Query: 234 FSPERLMADALANHAKGAAIL-------------EPTPLVTDWVSGVSLALALMFGPAGL 280 +P + + G +L + T V + ++ V L+LM G AGL Sbjct: 202 GNPIPMFGMFSTHTESGVPLLAKLDEVVTALGFRDYTADVDNKLNMVLFTLSLMIGTAGL 261 Query: 281 PHILMRFFTVPDAKEARKSVFYATGFVAYFFVLTTTIGFLA 321 PH+++RFFTVP +AR S +A F+A ++ +G +A Sbjct: 262 PHVIIRFFTVPKVADARWSAGWALVFIALLYLTAPAVGSMA 302 Score = 71.6 bits (174), Expect = 8e-17 Identities = 45/121 (37%), Positives = 72/121 (59%), Gaps = 2/121 (1%) Query: 358 LGFISAVAFATILAVVSGLALSGASAVAHDLYANVVKKGAAADKAEMRVSRIATLVLGVL 417 +G I+A A L+ +GL L+ +SA++HDL N + + ++K EM +RI+ +L Sbjct: 404 IGLIAAGGIAAALSTAAGLLLAISSAISHDLIKNTINP-SISEKGEMLAARISMAGAILL 462 Query: 418 AIVLGLMFENQNIAFMVGLAFGLAASVNFPVLLLSIFWKGMTTRGAFIGGLIGLVVSIVL 477 A LGL A +V LAFG+AA+ FPVL++ IF M ++GA G L GL+ +++ Sbjct: 463 ATYLGLNPPGF-AAQVVALAFGIAAASLFPVLMMGIFSTRMNSKGAICGMLAGLISTLLY 521 Query: 478 V 478 + Sbjct: 522 I 522 Lambda K H 0.328 0.140 0.414 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: 828 Number of extensions: 49 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 551 Length of database: 598 Length adjustment: 36 Effective length of query: 515 Effective length of database: 562 Effective search space: 289430 Effective search space used: 289430 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 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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