Align Phenylacetate permease, Ppa (characterized)
to candidate AZOBR_RS19235 AZOBR_RS19235 actetate permease
Query= TCDB::O50471 (520 letters) >FitnessBrowser__azobra:AZOBR_RS19235 Length = 556 Score = 691 bits (1782), Expect = 0.0 Identities = 341/520 (65%), Positives = 417/520 (80%) Query: 1 MNWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFL 60 +N TAI+MF++FV TL +T WA+ RTRSASDFYTAGGG++G QNGLAIAGD +SAA+FL Sbjct: 37 VNVTAIAMFLLFVAGTLGITYWASKRTRSASDFYTAGGGISGFQNGLAIAGDYMSAAAFL 96 Query: 61 GISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTS 120 G+S M+F G+DG++Y +G L GWP++LFLIAERLRNLG++TFADV SYRL QTP+R + Sbjct: 97 GLSGMVFAKGFDGVIYTIGFLVGWPLMLFLIAERLRNLGRFTFADVASYRLGQTPIRSLA 156 Query: 121 AFGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQII 180 A G+L V YL+AQMVGAGKLI+LLFG+ Y YAV++VGVLM+ YVTFGGMLATTWVQII Sbjct: 157 AVGSLTVVCFYLIAQMVGAGKLIQLLFGLDYTYAVVMVGVLMILYVTFGGMLATTWVQII 216 Query: 181 KAVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLG 240 KAVMLL G + + + L FGF+ E + AVA HA AI+ P +++P+ A+SL L Sbjct: 217 KAVMLLGGCTVLVGLALAQFGFNPERLLQQAVAAHAANAAILRPSAAMADPIAAVSLSLA 276 Query: 241 MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSYR 300 +M G AGLPHILMRFFTV DAKEARKSV YATGFIGYF++L + IGF AIV+VGT P+Y Sbjct: 277 LMCGPAGLPHILMRFFTVPDAKEARKSVVYATGFIGYFFILTVTIGFLAIVIVGTNPAYL 336 Query: 301 DATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDLYAC 360 DA G I+GGGNM A+HL++A+GGNLFLGFISAVAFATILAVVAGL L+GASAVSHDLYA Sbjct: 337 DAAGKILGGGNMAAIHLSKAIGGNLFLGFISAVAFATILAVVAGLTLAGASAVSHDLYAR 396 Query: 361 VIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPVLLL 420 V+++G ATE EMRVSR+ATL +G++A+ LGL+FE+QNIAF+ GL +AASVNFPVL+L Sbjct: 397 VLKKGNATEASEMRVSRLATLALGVIAITLGLLFENQNIAFMVGLAFGLAASVNFPVLIL 456 Query: 421 SMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSLAFL 480 S+FWKGLTTRGA G AGL S V VVLGP VWV+V +FPY +PALFSM +AF Sbjct: 457 SIFWKGLTTRGAFIGGFAGLVSCVAFVVLGPTVWVSVFKFPAPIFPYEHPALFSMVIAFA 516 Query: 481 SAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520 + W+FSVTD S RA+ E Y Q+IRS TG+GAA A+ H Sbjct: 517 TTWLFSVTDRSARAAAEAKAYEYQYIRSETGLGAASAASH 556 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: 901 Number of extensions: 49 Number of successful extensions: 1 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: 556 Length adjustment: 35 Effective length of query: 485 Effective length of database: 521 Effective search space: 252685 Effective search space used: 252685 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