Align Acetate permease; SubName: Full=Actetate permease; SubName: Full=Cation acetate symporter; SubName: Full=Cation/acetate symporter (characterized, see rationale)
to candidate BPHYT_RS25605 BPHYT_RS25605 symporter
Query= uniprot:A0A1N7U9G2 (552 letters) >FitnessBrowser__BFirm:BPHYT_RS25605 Length = 516 Score = 412 bits (1060), Expect = e-119 Identities = 220/519 (42%), Positives = 334/519 (64%), Gaps = 21/519 (4%) Query: 33 LNVSAIVMFVVFVGATLCITYWASKRNKSAADYYAAGGKITGFQNGLAIAGDYMSAASFL 92 + + IV+F++ + TL ITYWA++R ++ +++YAAGG ++ +NG A+AGD+MSAA+FL Sbjct: 1 MKLLTIVIFMIILAVTLMITYWAARRTRTTSEFYAAGGNLSARENGFALAGDWMSAAAFL 60 Query: 93 GISALVYTSGYDGLIYSIGFLVGWPIILFLIAERLRNLGKYTFADVASYRLGQTQIRSLS 152 G S LV G DG +Y++ L + ++L LIAE +RN G+YTF DV + R+ + R + Sbjct: 61 GFSGLVSLYGMDGSLYAVAALAAFLVVLMLIAEPVRNTGRYTFGDVIAERMKRPGARLAT 120 Query: 153 ACGSLVVVAFYLIAQMVGAGKLIQLLFGLDYHVAVILVGILMVLYVLFGGMLATTWVQII 212 G++VV Y++ QM GAG LI+L+ G+ Y VAV+LVGI M++YVLFGGM+ATTWVQI+ Sbjct: 121 IVGTVVVNLAYMVPQMAGAGALIKLMLGVPYDVAVVLVGIGMIVYVLFGGMIATTWVQIV 180 Query: 213 KAVLLLSGASFMALMVMKHVNFDFNALFSEAIKVHPKGEAIMSPGGLVKDPISAFSLGLA 272 KA+LLL A + M++ V F+ ALF+ +++ G +++ GG P+ SL ++ Sbjct: 181 KAMLLLVAACVLVSMLLAAVRFNPLALFASVERLY--GSKMLASGGYFHHPLDTMSLFIS 238 Query: 273 LMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYILTFIIGFGAILLVSTNPAFK 332 +FG AGLPHI+ RF+TV DA+ ARKSV + G F+++T +IGF + + V + Sbjct: 239 FIFGVAGLPHIMTRFYTVPDARTARKSVLWLMFLAGSFFMVTTLIGFASAVFVG-----Q 293 Query: 333 DAAGALMGGNNMAAVHL-------ANAVGGSIFLGFISAVAFATILAVVAGLTLAGASAV 385 DA A G N+A L A ++GG IFL I A+AFA ILAVVAGLTLA + A+ Sbjct: 294 DAIRAADKGGNLALPLLAQYLGGGAGSLGGQIFLASICAIAFAAILAVVAGLTLASSGAI 353 Query: 386 SHDLYASVIKKGKANDKDEIRVSKITTIALGVLAIGLGILFESQNIAFMVGLAFSIAASC 445 +HDLY +V++KG +D +++RV++I T+A+G+ AIGL +L + N+ +V LA S+AAS Sbjct: 354 AHDLYVNVLRKGAVSDAEQVRVARIATVAVGIAAIGLSLLAQGLNVGVLVILAISVAASS 413 Query: 446 NFPVLLLSMYWKNLTTRGAMIGGWLGLVSAVGLMVLGPTIWVSILHHEKAIFPYEYPALF 505 NFP++LLS++W+ T G + G GL S+V L +GP S A+FP PA+ Sbjct: 414 NFPIILLSIFWRRFNTAGVIGGVIGGLTSSVALAFVGPAFMGS-----HALFPIVNPAIV 468 Query: 506 SMIIAFVGIWFFSITDKSSAAEKERALYFPQFVRSQTGL 544 S+ I W ++ + + + F ++R+QTG+ Sbjct: 469 SLPIGLFSAWLCTMLSRPTPTQDGDFEAF--YLRAQTGI 505 Lambda K H 0.327 0.140 0.415 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: 801 Number of extensions: 56 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: 552 Length of database: 516 Length adjustment: 35 Effective length of query: 517 Effective length of database: 481 Effective search space: 248677 Effective search space used: 248677 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: 52 (24.6 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