Align Acetate permease; SubName: Full=Actetate permease; SubName: Full=Cation acetate symporter; SubName: Full=Cation/acetate symporter (characterized, see rationale)
to candidate AZOBR_RS19235 AZOBR_RS19235 actetate permease
Query= uniprot:A0A1N7U9G2 (552 letters) >FitnessBrowser__azobra:AZOBR_RS19235 Length = 556 Score = 731 bits (1886), Expect = 0.0 Identities = 367/552 (66%), Positives = 444/552 (80%), Gaps = 3/552 (0%) Query: 4 RLLAILGASIFAPAVWA---ADALTGEVHKQPLNVSAIVMFVVFVGATLCITYWASKRNK 60 RLLA A++ V A A+ G V +QP+NV+AI MF++FV TL ITYWASKR + Sbjct: 5 RLLAAASAALLPVLVAGPVHAAAIDGAVERQPVNVTAIAMFLLFVAGTLGITYWASKRTR 64 Query: 61 SAADYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIIL 120 SA+D+Y AGG I+GFQNGLAIAGDYMSAA+FLG+S +V+ G+DG+IY+IGFLVGWP++L Sbjct: 65 SASDFYTAGGGISGFQNGLAIAGDYMSAAAFLGLSGMVFAKGFDGVIYTIGFLVGWPLML 124 Query: 121 FLIAERLRNLGKYTFADVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFG 180 FLIAERLRNLG++TFADVASYRLGQT IRSL+A GSL VV FYLIAQMVGAGKLIQLLFG Sbjct: 125 FLIAERLRNLGRFTFADVASYRLGQTPIRSLAAVGSLTVVCFYLIAQMVGAGKLIQLLFG 184 Query: 181 LDYHVAVILVGILMVLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALF 240 LDY AV++VG+LM+LYV FGGMLATTWVQIIKAV+LL G + + + + F+ L Sbjct: 185 LDYTYAVVMVGVLMILYVTFGGMLATTWVQIIKAVMLLGGCTVLVGLALAQFGFNPERLL 244 Query: 241 SEAIKVHPKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSV 300 +A+ H AI+ P + DPI+A SL LALM G AGLPHILMRFFTV DAKEARKSV Sbjct: 245 QQAVAAHAANAAILRPSAAMADPIAAVSLSLALMCGPAGLPHILMRFFTVPDAKEARKSV 304 Query: 301 FYATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAGALMGGNNMAAVHLANAVGGSIFLG 360 YATGFIGYF+ILT IGF AI++V TNPA+ DAAG ++GG NMAA+HL+ A+GG++FLG Sbjct: 305 VYATGFIGYFFILTVTIGFLAIVIVGTNPAYLDAAGKILGGGNMAAIHLSKAIGGNLFLG 364 Query: 361 FISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANDKDEIRVSKITTIALGVLAI 420 FISAVAFATILAVVAGLTLAGASAVSHDLYA V+KKG A + E+RVS++ T+ALGV+AI Sbjct: 365 FISAVAFATILAVVAGLTLAGASAVSHDLYARVLKKGNATEASEMRVSRLATLALGVIAI 424 Query: 421 GLGILFESQNIAFMVGLAFSIAASCNFPVLLLSMYWKNLTTRGAMIGGWLGLVSAVGLMV 480 LG+LFE+QNIAFMVGLAF +AAS NFPVL+LS++WK LTTRGA IGG+ GLVS V +V Sbjct: 425 TLGLLFENQNIAFMVGLAFGLAASVNFPVLILSIFWKGLTTRGAFIGGFAGLVSCVAFVV 484 Query: 481 LGPTIWVSILHHEKAIFPYEYPALFSMIIAFVGIWFFSITDKSSAAEKERALYFPQFVRS 540 LGPT+WVS+ IFPYE+PALFSM+IAF W FS+TD+S+ A E Y Q++RS Sbjct: 485 LGPTVWVSVFKFPAPIFPYEHPALFSMVIAFATTWLFSVTDRSARAAAEAKAYEYQYIRS 544 Query: 541 QTGLGSSGAVSH 552 +TGLG++ A SH Sbjct: 545 ETGLGAASAASH 556 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: 966 Number of extensions: 52 Number of successful extensions: 2 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: 556 Length adjustment: 36 Effective length of query: 516 Effective length of database: 520 Effective search space: 268320 Effective search space used: 268320 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: 53 (25.0 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