Align Phenylacetate permease, Ppa (characterized)
to candidate PP_2797 PP_2797 acetate permease
Query= TCDB::O50471 (520 letters) >FitnessBrowser__Putida:PP_2797 Length = 552 Score = 620 bits (1600), Expect = 0.0 Identities = 305/523 (58%), Positives = 400/523 (76%), Gaps = 3/523 (0%) Query: 1 MNWTAISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFL 60 +N AI MFMVFV FTL +T WAA RTRS +DFY+AGGG+ G QNGLA+AGD +SA++ L Sbjct: 30 LNLHAIGMFMVFVLFTLCITWWAARRTRSTTDFYSAGGGIQGWQNGLALAGDYMSASTLL 89 Query: 61 GISAMMFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTS 120 GI+A+++ +G DG +Y + AGWP++L L+ ERLRNLG++TFAD+ SYRL Q VR + Sbjct: 90 GITALIYTSGMDGYIYLIAFFAGWPVLLLLMTERLRNLGRFTFADITSYRLDQGKVRTMA 149 Query: 121 AFGTLVVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQII 180 A G+L V YLVAQMVGAG+LI LLFG+ Y AV++VG LM+ YVTFGGM+ATTWVQII Sbjct: 150 AIGSLTVVCFYLVAQMVGAGQLIRLLFGLDYHIAVVIVGALMMLYVTFGGMVATTWVQII 209 Query: 181 KAVMLLSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLG 240 KA +LL G S + F+ ++ F FS +A+ + A+ HA G+ ++APG LL++P+ A+SL LG Sbjct: 210 KAFLLLVGGSLVLFLAMREFDFSYDALVSKAMDTHALGERLLAPGSLLADPLTALSLSLG 269 Query: 241 MMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVGTEPSY- 299 ++FGTAGLPHILMRFFTVSDA+EARKSV YATGFIGYF+ ++ ++G +IV+V +P + Sbjct: 270 LVFGTAGLPHILMRFFTVSDAREARKSVLYATGFIGYFFNVIFLLGLASIVIVSQQPKFF 329 Query: 300 --RDATGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHDL 357 + G ++GGGNM+ +HLAQAVGGNL LGF+SAV FATILAVV+GLAL+GASA++HDL Sbjct: 330 EGGEVGGKLLGGGNMVVMHLAQAVGGNLLLGFLSAVTFATILAVVSGLALAGASAIAHDL 389 Query: 358 YACVIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFPV 417 YA VI +G A+E +E+RV+++ATL +GL+A+ LG++FE+ N+AF+ L +AAS NFPV Sbjct: 390 YARVIMKGAASEAQELRVTKLATLSLGLVAIALGILFENINVAFMVALAFGIAASANFPV 449 Query: 418 LLLSMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVNVLHHEKALFPYSNPALFSMSL 477 L LSMFW GLTTRGA+ GL SA+ VV VWV+VLH + LFPY+ PALFSM L Sbjct: 450 LFLSMFWSGLTTRGALAAGYVGLLSAMGFVVFSKLVWVDVLHFAEPLFPYTQPALFSMPL 509 Query: 478 AFLSAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520 AFL A+ S D + RA ER + QF+R TG+GA+GA H Sbjct: 510 AFLVAYAVSRMDRTARAKAERAAFADQFVRGQTGLGASGAVDH 552 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: 872 Number of extensions: 43 Number of successful extensions: 3 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: 552 Length adjustment: 35 Effective length of query: 485 Effective length of database: 517 Effective search space: 250745 Effective search space used: 250745 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