Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate Ga0059261_2514 Ga0059261_2514 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::WCS417:GFF780 (952 letters) >FitnessBrowser__Korea:Ga0059261_2514 Length = 759 Score = 279 bits (713), Expect = 6e-79 Identities = 191/570 (33%), Positives = 295/570 (51%), Gaps = 22/570 (3%) Query: 399 SQVQAIAAAPGIAIGPAHIQVLQVFDYPLRGESCAIERERLHSALADVRRDIQGLIERSQ 458 ++V G+A G A ++ E ER R+++A +R I + +++ Sbjct: 183 ARVPGFKLVEGMAAGAAVFHQPRIIIEHTVAEDIEAERHRVYAAFDKMREQIDRMTSQAE 242 Query: 459 ---SKAIREIFVTHQEMLDDPELTDEVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALL 515 E+ T++ D + ++ + G +AEAA V + + + D LL Sbjct: 243 FGGGGEHEEVLETYKMFAYDEGWSRRINEAIDSGLTAEAAIERVQQRTRMRMRQIDDPLL 302 Query: 516 AERAADLRDIGRRVLAQLCG-VETSQEPS--EPYILVMDEVGPSDVARLDPARVAGILTA 572 +R DL D+ R+L + G + T+ + + IL+ +GP+++ D R+ G++ Sbjct: 303 RDRMHDLEDLSNRLLRIVSGQLGTAAQLGLRQDSILIARNLGPAELLEYDRRRLKGVVLE 362 Query: 573 RGGATAHSAIVARALGIPALVGAGPAVLLLAAGTPLLLDGQRGRLHVDADAATLQRATVE 632 G TAH IVARA+G+P L L+A G LL+D L + AA + + Sbjct: 363 EGSLTAHVTIVARAMGVPVLGRVKDIRRLIAEGDRLLVDVTEDTLIIRPTAAMDEAFEAK 422 Query: 633 RDTREQRLQAASAQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFM 692 ++R A +A ++E +T DGH + V N G VA+ GA+GIGL RTE F+ Sbjct: 423 LLVTQKRRAAFAALKNEAPVTTDGHRLTVMVNAGLRDDVAALDLTGADGIGLFRTEFQFL 482 Query: 693 AHPQAPDEATQEAEYRRVLDGLAGRPLVVRTLDVGGDKPLPYW---PIAEEENPFLGVRG 749 P +Q Y+ VLD RP+ RT+D+GGDK LPY EEENP +G R Sbjct: 483 VSATLPQRDSQRRLYKDVLDAAGDRPVTFRTVDIGGDKALPYLDHDENGEEENPAMGWRA 542 Query: 750 IRLTLQRPQIMEAQLRALLRSADNRPLRIMFPMVGSVDEWRAARDM--TERLRLE----- 802 +RL L R +M+ Q RALL +A R L +MFPMV E+ AR + T+R LE Sbjct: 543 LRLALDREGLMKVQARALLEAAAGRTLNVMFPMVSEPWEFDEARTLFETQRAWLESRGHK 602 Query: 803 IPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLH 862 +P+ ++ G M+EVP+ A + +L +DF SVGTNDLTQ+ A DR HP L+ + D L Sbjct: 603 LPL-HIRYGAMLEVPALAEVLDLLLPRLDFLSVGTNDLTQFLFAADRAHPKLAVRYDWLS 661 Query: 863 PAVLQLI-DITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIPEVKARV 921 P++L+ + +T AA A + VCGE+ PL L+GLG+D LS++ ++ +KA V Sbjct: 662 PSILRFLRRVTAEAAEADVP-LAVCGEMGGRPLEAMALIGLGIDRLSITPAAVGPIKAMV 720 Query: 922 REFSLSEAQGL-AQKALAVGSPAEVRALVE 950 R SL A+ + A + + P ++RA +E Sbjct: 721 R--SLDRAKLIAAMRGMLDRPPQDMRAALE 748 Lambda K H 0.318 0.135 0.385 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: 1393 Number of extensions: 62 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: 952 Length of database: 759 Length adjustment: 42 Effective length of query: 910 Effective length of database: 717 Effective search space: 652470 Effective search space used: 652470 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 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