Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate RR42_RS06400 RR42_RS06400 acetate permease
Query= SwissProt::P32705 (549 letters) >FitnessBrowser__Cup4G11:RR42_RS06400 Length = 546 Score = 694 bits (1791), Expect = 0.0 Identities = 358/537 (66%), Positives = 426/537 (79%), Gaps = 2/537 (0%) Query: 5 LTALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSRSDYY 64 L A+ A L A A A G+V Q N AI MFL+FV TL +T WA++ S +D+Y Sbjct: 6 LCAIGAALLLTALPAFAAPGSVG-QGMNVIAIAMFLMFVAATLVVTRWAARSNHSVADHY 64 Query: 65 TAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFLIAER 124 AGG IT QNG AIAGDYMSAAS LGISALVFTSGYDGLIYS+GFL WPIILFLIAE Sbjct: 65 AAGGKITALQNGWAIAGDYMSAASLLGISALVFTSGYDGLIYSIGFLASWPIILFLIAEP 124 Query: 125 LRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLNYHIA 184 LRNLGR+T ADV SYRL+Q PIR SA S+V+V LYL++QMVGAGKL+ELLFG +Y A Sbjct: 125 LRNLGRFTLADVVSYRLRQRPIRAFSASSSIVIVLLYLVSQMVGAGKLVELLFGFSYTAA 184 Query: 185 VVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAV 244 VVLVGVLM++YV FGGMLATTW+QIIKAVLLL GA+FMAFMVM GFS N LF++A+ Sbjct: 185 VVLVGVLMVVYVFFGGMLATTWIQIIKAVLLLAGAAFMAFMVMSRFGFSLNALFAQAIEA 244 Query: 245 HPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFYATGF 304 H K IM+PGGLV DP+SA+SLGL L+FGTAGLPHILMRFFTV D + ARKS+ YATG Sbjct: 245 HGKHAAIMRPGGLVSDPVSAVSLGLALIFGTAGLPHILMRFFTVGDVKAARKSILYATGI 304 Query: 305 MGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGFISAVA 364 +G Y L IIGFG I LV ++P Y AG +IGG NM AVHLA+AVGGNLFLGFI AVA Sbjct: 305 VGIGYALIIIIGFGTIALVASDPAYHTPAGAVIGGVNMVAVHLAHAVGGNLFLGFICAVA 364 Query: 365 FATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAIILGVLF 423 F+TILAVVAGLTLAG+SA+SHDLYA V ++G AT++EE+RVS++T L+LGV++I+LG+LF Sbjct: 365 FSTILAVVAGLTLAGSSAISHDLYAKVLRQGNATDKEEMRVSRMTTLVLGVLSILLGILF 424 Query: 424 ENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMILGPTIW 483 E Q IAF+V L F+IAAS NFP++LLS+YW LTTRGA++GG LGL++AVVL +L PT+W Sbjct: 425 EKQTIAFIVSLTFSIAASSNFPVLLLSIYWRGLTTRGAVVGGSLGLLSAVVLTVLSPTVW 484 Query: 484 VQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQTG 540 VQ+LGH +AI+PYEYPALFS+ VAF GI+ FS TD SA GARER F Q + + G Sbjct: 485 VQVLGHARAIYPYEYPALFSMLVAFAGIYVFSVTDRSARGARERGAFNNQLVDCELG 541 Lambda K H 0.329 0.142 0.424 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: 888 Number of extensions: 42 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: 549 Length of database: 546 Length adjustment: 36 Effective length of query: 513 Effective length of database: 510 Effective search space: 261630 Effective search space used: 261630 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 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