Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate GFF475 HP15_463 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain protein
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__Marino:GFF475 Length = 768 Score = 274 bits (701), Expect = 1e-77 Identities = 192/624 (30%), Positives = 319/624 (51%), Gaps = 21/624 (3%) Query: 222 IMGLGVAEQDEVEVICRGEDSEAALGALLAALASATAGAPKDAPRAIAPGEPARPAAVAG 281 ++G+ V +Q E C E EA L + A LA A + +A AI+ A Sbjct: 121 VLGVLVVQQRESSR-CFDEGEEAFLVTVSAQLAGVIAHS--EATGAISGLSLTGEEAHDV 177 Query: 282 TLAGVCASPGLASGPLARLGAISLPADDGRHRPEEQHLALDQAL-------QRVRDDVQG 334 + GV +PG+A G G + P+ D PE+ +DQ L + VR+D++ Sbjct: 178 SFNGVPGAPGVAIGN----GVVVYPSADLDVVPEKPTDDIDQELALFGASVKAVREDIER 233 Query: 335 SLQQARLGGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQA 394 ++ E A+F +L +L D + I +G+ A A + +Q + Sbjct: 234 VAKRLASQLRPEEQALFDVYLRMLGDDAMPGEVSNKIREGIWAQGALKQVVQQYIRHFEM 293 Query: 395 LGNLLLAERANDLRDLEKRVLRVLL-GDTAPLRVPAGAIVAAREITPSDLAPLVDAGAAG 453 + + L ERA D+RDL +R+L L G+ L P ++ + E+TP+ L + G Sbjct: 294 MDDHYLQERAVDIRDLGRRLLSHLQEGEQKHLNYPERTVLVSEELTPAMLGEVPKGQLVG 353 Query: 454 LCMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQ 513 L +G + SHVAILAR+ G+P ++ L + +G+++++D +G++ SP A Sbjct: 354 LVSVKGSSNSHVAILARAMGVPTVMGLVDIPVNQLDGKELIVDGFEGQIFASPSADLRSY 413 Query: 514 VALQVAQREEQRRRQQADAQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTE 573 + +E R + + T D R+ + N + + ++GA+G+GL RTE Sbjct: 414 YQAICDEEDELIRGLEVLKDKPCETTDHHRVSLLVNTGLMTDVVRSLSHGAEGIGLYRTE 473 Query: 574 FLFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLR 633 F+ + P E+EQR Y+E L+A V +RT+D+GGDK L Y P+ EENP LG R Sbjct: 474 VPFMIKDRFPSEQEQREYYREQLEAFAPSPVTMRTLDIGGDKALTYFPIQ-EENPFLGWR 532 Query: 634 GIHLGQARPELLDQQLRALLRV-EPLERCRILLPMVSEVDE----LRAIRRRLGELATQL 688 GI + PE+ Q+RA+L+ E L +I+LPM+S + E L I R E+ + Sbjct: 533 GIRVTLDHPEIFLVQVRAMLKASEGLNNLQIMLPMISNISEVEESLHLIYRVYHEVREEG 592 Query: 689 GIERLPELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALH 748 +P++GVM+E+P+A +LA+ DFLS+G+NDL+QY LA+DR + +A + H Sbjct: 593 YDIHMPKVGVMVEIPAAVYQIRELADRVDFLSVGSNDLTQYLLAVDRNNPRVAQLYHSYH 652 Query: 749 PALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVR 808 PA+L+ + + A G+ VG+CG LA DP +L+ +G + LS+ + ++K+ +R Sbjct: 653 PAVLQALVRIAQDAHSVGKPVGICGELAGDPGGALLLMAMGYDSLSMNAASLPKVKSVIR 712 Query: 809 QLDAAECRRHAQALLDLGSARAVR 832 + + + +L L S ++ Sbjct: 713 SVSREWAIQLLEDVLLLDSPHVIK 736 Lambda K H 0.319 0.136 0.390 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: 1284 Number of extensions: 59 Number of successful extensions: 6 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: 842 Length of database: 768 Length adjustment: 41 Effective length of query: 801 Effective length of database: 727 Effective search space: 582327 Effective search space used: 582327 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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