Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate PP_5145 PP_5145 phosphoenolpyruvate-dependent regulator (with NPR and NTR proteins)
Query= reanno::WCS417:GFF780 (952 letters) >FitnessBrowser__Putida:PP_5145 Length = 759 Score = 328 bits (842), Expect = 6e-94 Identities = 201/561 (35%), Positives = 320/561 (57%), Gaps = 16/561 (2%) Query: 404 IAAAPGIAIGPAHIQV----LQVFDYPLRGESCAIERERLHSALADVRRDIQGLIERSQS 459 + +PG A+G A + + L+V + A E + +AL VR D++ L + + Sbjct: 181 VPGSPGAAVGRAVVMLPPADLEVVPDKTVDDIDA-ELKLFQNALEGVRDDMRKLSAKLAT 239 Query: 460 KAI---REIFVTHQEMLDDPELTDEVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLA 516 + R +F + ML+D L EV +K G+ A+ A V+ + E + D L Sbjct: 240 QLRPEERALFDVYLMMLEDAALGGEVTEVIKTGQWAQGALRQVVGEHVNRFELMDDDYLR 299 Query: 517 ERAADLRDIGRRVLAQLCGVET-SQEPSEPYILVMDEVGPSDVARLDPARVAGILTARGG 575 ERA+D++D+GRR+LA L + S ++ ILV +E+ P+ + + ++ G+++ G Sbjct: 300 ERASDVKDLGRRLLAYLQEARSQSLVYADNTILVSEELTPAMLGEVPEGKLVGLVSVLGS 359 Query: 576 ATAHSAIVARALGIPALVGAGPAVLLLAAGTPLLLDGQRGRLHVDADAATLQRATVERDT 635 +H AI+ARA+GIP ++G G L++DG +G + + ++ + + Sbjct: 360 GNSHVAILARAMGIPTVMGLVDLPYSKVDGIELIVDGYKGEVFTNPSEVLRKQYSEVVEE 419 Query: 636 REQRLQAASAQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHP 695 Q Q A R P +T DGH + ++ N G A VA A ++GAEG+GL RTE+ FM + Sbjct: 420 ERQLAQGLDALRELPCVTPDGHRMPLWVNTGLLADVARAQQRGAEGVGLYRTEVPFMINQ 479 Query: 696 QAPDEATQEAEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAEEENPFLGVRGIRLTLQ 755 + P E Q A YR L P+ +RTLD+GGDK L Y+PI +EENPFLG RGIR+TL Sbjct: 480 RFPSEKEQLAIYREQLAAFHPLPVTMRTLDIGGDKALSYFPI-KEENPFLGWRGIRVTLD 538 Query: 756 RPQIMEAQLRALLRSADN-RPLRIMFPMVGSVDEWRAARDMTERLRLEI-----PVADLQ 809 P+I Q RA+L++++ LRI+ PM+ + E A + R E+ V Sbjct: 539 HPEIFLVQTRAMLKASEGLNNLRILLPMISGIHELEEALHLIHRAWGEVRDEGTDVPMPP 598 Query: 810 LGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLI 869 +G+M+E+P+A LA++VDF SVG+NDLTQY LA+DR +P ++ D LHPAVLQ + Sbjct: 599 VGVMVEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYLHPAVLQAL 658 Query: 870 DITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIPEVKARVREFSLSEA 929 + VR AH GK V +CGE+A DP A +L+ +G D LS++A ++P+VK +R+ ++ +A Sbjct: 659 NTVVRDAHGEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWMLRQINMGKA 718 Query: 930 QGLAQKALAVGSPAEVRALVE 950 + L +AL+ +P + + ++ Sbjct: 719 KELLAEALSHDNPQVIHSSLQ 739 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: 1442 Number of extensions: 77 Number of successful extensions: 4 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