Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate PP_2797 PP_2797 acetate permease
Query= reanno::PV4:5209923 (572 letters) >FitnessBrowser__Putida:PP_2797 Length = 552 Score = 170 bits (430), Expect = 2e-46 Identities = 148/550 (26%), Positives = 247/550 (44%), Gaps = 64/550 (11%) Query: 1 MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60 +++ + +V F L I R ST +FY AGGG+ NG+A A D+MSA++ + Sbjct: 30 LNLHAIGMFMVFVLFTLCITWWAARRTRSTTDFYSAGGGIQGWQNGLALAGDYMSASTLL 89 Query: 61 SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120 + ++ G DG +YL+ + G+ +L L M LR G+FT D R RT+A Sbjct: 90 GITALIYTSGMDGYIYLIAFFAGWPVLLLLMTERLRNLGRFTFADITSYRLDQGKVRTMA 149 Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180 + ++ + Y+ QM G G + ++ V I A++ Y GGM T+ Q+ Sbjct: 150 AIGSLTVVCFYLVAQMVGAGQLIRLLFGLDYHIAVVIVGALMMLYVTFGGMVATTWVQII 209 Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNN---TGVYLLEKLDGLSAQL 237 + +L+ + +F+++ L A A G G L + L LS L Sbjct: 210 KAFLLLVGGSL-VLFLAMREFDFSYDALVSKAMDTHALGERLLAPGSLLADPLTALSLSL 268 Query: 238 GFSQYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMY 297 G L+FGTAGLPH+++RFFTV ++AR S +A FI + Sbjct: 269 G--------------------LVFGTAGLPHILMRFFTVSDAREARKSVLYATGFIGYFF 308 Query: 298 TTIPALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKG 357 I L S V + + P + + E G + G Sbjct: 309 NVIFLLGLASIVIVSQ--------------QPKFFEGGEVGGKL--------------LG 340 Query: 358 ETNEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKK 417 N + +M LA NL ++ ++A A L+ +GL L +++++HDL + Sbjct: 341 GGNMV-----VMHLAQAVGGNL---LLGFLSAVTFATILAVVSGLALAGASAIAHDLYAR 392 Query: 418 NFMPD-ISDKQELLYARIAA-ALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIM 475 M S+ QEL ++A +LG+V + VA +VA+AFG+AAS+ FP + + Sbjct: 393 VIMKGAASEAQELRVTKLATLSLGLVAIALGILFENINVAFMVALAFGIAASANFPVLFL 452 Query: 476 GIFSRTMNKEGAIAGMVIGLLFSASYIIYFKFVNPGDNNASNWLFGISPEGIGMLGMIIN 535 +F + GA+A +GLL + ++++ K V + + LF + + M + Sbjct: 453 SMFWSGLTTRGALAAGYVGLLSAMGFVVFSKLVWVDVLHFAEPLFPYTQP--ALFSMPLA 510 Query: 536 FAVAFIVSKV 545 F VA+ VS++ Sbjct: 511 FLVAYAVSRM 520 Lambda K H 0.326 0.140 0.423 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: 783 Number of extensions: 41 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 572 Length of database: 552 Length adjustment: 36 Effective length of query: 536 Effective length of database: 516 Effective search space: 276576 Effective search space used: 276576 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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