Align Phenylacetate permease, Ppa (characterized)
to candidate RR42_RS06400 RR42_RS06400 acetate permease
Query= TCDB::O50471 (520 letters) >FitnessBrowser__Cup4G11:RR42_RS06400 Length = 546 Score = 665 bits (1717), Expect = 0.0 Identities = 330/512 (64%), Positives = 407/512 (79%) Query: 1 MNWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFL 60 MN AI+MF++FV TL+VTRWAA S +D Y AGG +T +QNG AIAGD +SAAS L Sbjct: 31 MNVIAIAMFLMFVAATLVVTRWAARSNHSVADHYAAGGKITALQNGWAIAGDYMSAASLL 90 Query: 61 GISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTS 120 GISA++F +GYDGL+Y++G LA WPIILFLIAE LRNLG++T ADVVSYRL Q P+R S Sbjct: 91 GISALVFTSGYDGLIYSIGFLASWPIILFLIAEPLRNLGRFTLADVVSYRLRQRPIRAFS 150 Query: 121 AFGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQII 180 A ++V+ L+YLV+QMVGAGKL+ELLFG SY AV+LVGVLMV YV FGGMLATTW+QII Sbjct: 151 ASSSIVIVLLYLVSQMVGAGKLVELLFGFSYTAAVVLVGVLMVVYVFFGGMLATTWIQII 210 Query: 181 KAVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLG 240 KAV+LL+G +FMAFMV+ FGFS A+FA A+ H K AIM PGGL+S+PV A+SLGL Sbjct: 211 KAVLLLAGAAFMAFMVMSRFGFSLNALFAQAIEAHGKHAAIMRPGGLVSDPVSAVSLGLA 270 Query: 241 MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYR 300 ++FGTAGLPHILMRFFTV D K ARKS+ YATG +G Y L+I+IGFG I +V ++P+Y Sbjct: 271 LIFGTAGLPHILMRFFTVGDVKAARKSILYATGIVGIGYALIIIIGFGTIALVASDPAYH 330 Query: 301 DATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYAC 360 GA+IGG NM+AVHLA AVGGNLFLGFI AVAF+TILAVVAGL L+G+SA+SHDLYA Sbjct: 331 TPAGAVIGGVNMVAVHLAHAVGGNLFLGFICAVAFSTILAVVAGLTLAGSSAISHDLYAK 390 Query: 361 VIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVLLL 420 V+RQG AT++EEMRVSR+ TL++G+L++LLG++FE Q IAF+ L ++AAS NFPVLLL Sbjct: 391 VLRQGNATDKEEMRVSRMTTLVLGVLSILLGILFEKQTIAFIVSLTFSIAASSNFPVLLL 450 Query: 421 SMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSLAFL 480 S++W+GLTTRGAV G GL SAV+L VL P VWV VL H +A++PY PALFSM +AF Sbjct: 451 SIYWRGLTTRGAVVGGSLGLLSAVVLTVLSPTVWVQVLGHARAIYPYEYPALFSMLVAFA 510 Query: 481 SAWVFSVTDSSERASEERGRYLAQFIRSMTGI 512 +VFSVTD S R + ERG + Q + G+ Sbjct: 511 GIYVFSVTDRSARGARERGAFNNQLVDCELGL 542 Lambda K H 0.328 0.139 0.407 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: 835 Number of extensions: 37 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: 520 Length of database: 546 Length adjustment: 35 Effective length of query: 485 Effective length of database: 511 Effective search space: 247835 Effective search space used: 247835 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: 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