Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate GFF2318 PGA1_c23500 phosphoenolpyruvate-protein phosphotransferase PtsP
Query= reanno::BFirm:BPHYT_RS02740 (854 letters) >FitnessBrowser__Phaeo:GFF2318 Length = 746 Score = 226 bits (575), Expect = 5e-63 Identities = 157/513 (30%), Positives = 242/513 (47%), Gaps = 8/513 (1%) Query: 328 ESRLLDKAIATVDADLDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARDLISLGKS 387 E L +A+ + +D + + +Q G + + +R+ + + I G S Sbjct: 217 ELERLHEAVEELRVGVDKML-EVTQTGDKEQLQVLEAYRMFANSKGWMRRMEEDIGRGLS 275 Query: 388 AGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRAL-GYTSATARTLPEEAVLA 446 A A + A + ++DA L ER +DL D+ R+LR L G S T LPE+ VL Sbjct: 276 AEAAVEKEQSQARARMGQVQDAYLRERLSDLDDLSNRLLRILTGQGSETGAELPEDPVLI 335 Query: 447 AEEFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVV 506 A P +L R+ + +V+ G SHAAI+AR IP +V G ++ Sbjct: 336 ARNIGPGELLEYGRN-LRGIVLEEGSVGSHAAIIARALAIPLVVHTKRITTEALNGDHIM 394 Query: 507 VNATTGRLEFAPTELDVERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLD 566 V+ G + P + V R + A +E + A+T DGR + + N + Sbjct: 395 VDGEQGVVHLRPDDTVVSAFRDKIAMQAKAQERYASIRDKQALTRDGRRVHLLMNAGLMA 454 Query: 567 DAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGAD 626 D + +GA+ VGL RTEL F+ R P E YQ ++DA G+ + RTLD+G+D Sbjct: 455 DLPSLENSGAEGVGLFRTELQFLVRNQMPKRSELVALYQRVLDAAGGKRVVFRTLDIGSD 514 Query: 627 KEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGEL 686 K + Y+ EPNPALG R IR+ +P ++ QL+ L+ + ++ P V E Sbjct: 515 KVLPYMKPTDEPNPALGWRAIRVGLDKPGVMRMQLQALIRAANGRPLTVMFPFVAQFEEF 574 Query: 687 IRIRKRID---EFARELGRT--EPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQY 741 + ++ E R LG E +EVG M+E PS A + +FLSIG NDL Q+ Sbjct: 575 RDAKAEVEKTLERERRLGHALPEKLEVGAMLETPSLAFAPQKFFDEVEFLSIGGNDLKQF 634 Query: 742 TLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLG 801 A DR + + D L+ + L IA V+ +K G + CG AG P+ L +G Sbjct: 635 FFAADRENERVRKRYDTLNVSYLSFIAQIVERCEKSGTPLSFCGEDAGRPIEAVCLAAMG 694 Query: 802 VTELSVDPVSVPGIKARVRNLDYQLCRQRAQDA 834 + LS+ P SV +K+ + +D R+ DA Sbjct: 695 LRVLSMRPASVGPVKSLLMRVDLNDIRKIIADA 727 Lambda K H 0.317 0.133 0.371 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: 1210 Number of extensions: 58 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: 854 Length of database: 746 Length adjustment: 41 Effective length of query: 813 Effective length of database: 705 Effective search space: 573165 Effective search space used: 573165 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: 55 (25.8 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