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 AO356_10350 AO356_10350 phosphoenolpyruvate-protein phosphotransferase
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_10350 Length = 759 Score = 272 bits (696), Expect = 5e-77 Identities = 199/628 (31%), Positives = 314/628 (50%), Gaps = 26/628 (4%) Query: 222 IMGLGVAEQDEVEVICRGEDSEAALGALLAALASATAGAPKDAPRAIAPGEPARPAAVAG 281 ++G+ V +Q E GE EA L + A LA A A +A +I+ Sbjct: 121 VVGVLVIQQKERRQFDEGE--EAFLVTMSAQLAGVIAHA--EATGSISGLGRQGKGIQEA 176 Query: 282 TLAGVCASPGLASGPLARLGAISLPADDGRHRPEEQHLALDQ-------ALQRVRDDVQG 334 GV SPG A G + LP D P++ ++ A++ VR D++ Sbjct: 177 KFVGVPGSPGAAVGT----AVVMLPPADLDVVPDKTITDINAELGLFKTAIEGVRADMRA 232 Query: 335 SLQQARLGGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQA 394 + E A+F +L +L+D L +I G A A + + + Sbjct: 233 LSAKLATQLRPEERALFDVYLMMLDDASLGSEVTTVIKTGQWAQGALRQVVTDHVNRFEL 292 Query: 395 LGNLLLAERANDLRDLEKRVLRVLLGDTAPLRV-PAGAIVAAREITPSDLAPLVDAGAAG 453 + + L ERA+D++DL +R+L L + V P I+ + E+TP+ L + + AG Sbjct: 293 MDDAYLRERASDVKDLGRRLLAYLQQERQQTLVYPDNTILVSEELTPAMLGEVPEGKLAG 352 Query: 454 LCMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQ 513 L G SHVAILAR+ G+P ++ L +G Q+++D G + +P +Q Sbjct: 353 LVSVLGSGNSHVAILARAMGIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQ 412 Query: 514 VALQVAQREEQRRRQQADAQRE--ALTRDGRRIEIGANVASPREAAEAFANGADGVGLLR 571 A V EE++ DA R+ +T DG R+ + N + A A GA+GVGL R Sbjct: 413 FADVV--EEEKQLSLGLDALRDLPCVTLDGHRMPLWVNTGLLADVARAQKRGAEGVGLYR 470 Query: 572 TEFLFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALG 631 TE F+ + P E+EQ Y+E L A + V +R++D+GGDK L Y P+ E+NP LG Sbjct: 471 TEVPFMINQRFPSEKEQLAIYREQLAAFHPQPVTMRSLDIGGDKSLSYFPIK-EDNPFLG 529 Query: 632 LRGIHLGQARPELLDQQLRALLRV-EPLERCRILLPMVSEVDELRA----IRRRLGELAT 686 RGI + PE+ Q RA+L+ E L RILLPM+S EL I R GE+ Sbjct: 530 WRGIRVTLDHPEIFLVQARAMLKASEGLNNLRILLPMISGTHELEEALHLIHRAWGEVRD 589 Query: 687 QLGIERLPELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDA 746 + +P +GVMIE+P+A +LA DFLS+G+NDL+QY LA+DR + +AD D Sbjct: 590 EGTDVPMPPVGVMIEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDY 649 Query: 747 LHPALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTR 806 LHPA+L+ + A G+ V +CG +A DP A +L+ +G + LS+ + ++K Sbjct: 650 LHPAVLQALQNVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWM 709 Query: 807 VRQLDAAECRRHAQALLDLGSARAVRDA 834 +RQ++ ++ + ++ + + + + + Sbjct: 710 LRQINLSKAQELLAEVMTIDNPQVIHSS 737 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: 1282 Number of extensions: 65 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: 759 Length adjustment: 41 Effective length of query: 801 Effective length of database: 718 Effective search space: 575118 Effective search space used: 575118 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: 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