Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate Pf6N2E2_3942 FIG001592: Phosphocarrier protein kinase/phosphorylase, nitrogen regulation associated
Query= reanno::WCS417:GFF780 (952 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3942 Length = 759 Score = 334 bits (857), Expect = 1e-95 Identities = 205/565 (36%), Positives = 326/565 (57%), Gaps = 24/565 (4%) Query: 404 IAAAPGIAIGPAHIQVLQVFDYPLRGESCAIERER----LHSALADVRRDIQGLIERSQS 459 + +PG A+G A + +L D + + + + +A+ VR D++ L + + Sbjct: 181 VPGSPGAAVGTA-VVMLPPADLDVVPDKAITDIDAELGLFKTAIEGVRADMRALSAKLAT 239 Query: 460 KAI---REIFVTHQEMLDDPELTDEVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLA 516 + R +F + MLDD L EV T +K G+ A+ A V+ + E + DA L Sbjct: 240 QLRPEERALFDVYLMMLDDASLGSEVTTVIKTGQWAQGALRQVVTDHVNRFELMDDAYLR 299 Query: 517 ERAADLRDIGRRVLAQLCGVETSQEPSEPY----ILVMDEVGPSDVARLDPARVAGILTA 572 ERA+D++D+GRR+LA L + ++ + Y ILV +E+ P+ + + ++AG+++ Sbjct: 300 ERASDVKDLGRRLLAYL---QQERQQTLVYPDNTILVSEELTPAMLGEVPEGKLAGLVSV 356 Query: 573 RGGATAHSAIVARALGIPALVGAGPAVLLLAAGTPLLLDGQRGRLHVD-ADAATLQRATV 631 G +H AI+ARA+GIP ++G G +++DG G ++ + +D Q A V Sbjct: 357 LGSGNSHVAILARAMGIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQFADV 416 Query: 632 ERDTREQRLQAASAQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIF 691 + ++ L A R P +T DGH + ++ N G A VA A ++GAEG+GL RTE+ F Sbjct: 417 VEEEKQLSL-GLDALRDLPCVTLDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVPF 475 Query: 692 MAHPQAPDEATQEAEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAEEENPFLGVRGIR 751 M + + P E Q A YR L +P+ +R+LD+GGDK L Y+PI +E+NPFLG RGIR Sbjct: 476 MINQRFPSEKEQLAIYREQLAAFHPQPVTMRSLDIGGDKSLSYFPI-KEDNPFLGWRGIR 534 Query: 752 LTLQRPQIMEAQLRALLRSADN-RPLRIMFPMVGSVDEWRAARDMTERLRLEI-----PV 805 +TL P+I Q RA+L++++ LRI+ PM+ E A + R E+ V Sbjct: 535 VTLDHPEIFLVQARAMLKASEGLNNLRILLPMISGTHELEEALHLIHRAWGEVRDEGTDV 594 Query: 806 ADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAV 865 +G+MIE+P+A LA++VDF SVG+NDLTQY LA+DR +P ++ D LHPAV Sbjct: 595 PMPPIGVMIEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYLHPAV 654 Query: 866 LQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIPEVKARVREFS 925 LQ + VR AHA GK V +CGE+A DP A +L+ +G D LS++A ++P+VK +R+ + Sbjct: 655 LQALQNVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWMLRQIN 714 Query: 926 LSEAQGLAQKALAVGSPAEVRALVE 950 LS+AQ L + + + +P + + ++ Sbjct: 715 LSKAQELLAEVMTIDNPQVIHSSLQ 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: 1438 Number of extensions: 73 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