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 Ga0059261_2514 Ga0059261_2514 phosphoenolpyruvate-protein phosphotransferase
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__Korea:Ga0059261_2514 Length = 759 Score = 268 bits (685), Expect = 9e-76 Identities = 181/530 (34%), Positives = 261/530 (49%), Gaps = 19/530 (3%) Query: 324 ALQRVRDDVQGSLQQARLGGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHR 383 A ++R+ + QA GG + + D G + ID G+ A A R Sbjct: 226 AFDKMREQIDRMTSQAEFGGGGEHEEVLETYKMFAYDEGWSRRINEAIDSGLTAEAAIER 285 Query: 384 AIQAQCEILQALGNLLLAERANDLRDLEKRVLRVL---LGDTAPLRVPAGAIVAAREITP 440 Q ++ + + LL +R +DL DL R+LR++ LG A L + +I+ AR + P Sbjct: 286 VQQRTRMRMRQIDDPLLRDRMHDLEDLSNRLLRIVSGQLGTAAQLGLRQDSILIARNLGP 345 Query: 441 SDLAPLVDAGAAGLCMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQG 500 ++L G+ + EG T+HV I+AR+ G+P L + + EG ++++D + Sbjct: 346 AELLEYDRRRLKGVVLEEGSLTAHVTIVARAMGVPVLGRVKDIRRLIAEGDRLLVDVTED 405 Query: 501 RLELSPDARRLEQVALQVAQREEQRRRQQADAQREALTRDGRRIEIGANVASPREAAEAF 560 L + P A E ++ +++R A +T DG R+ + N + A Sbjct: 406 TLIIRPTAAMDEAFEAKLLVTQKRRAAFAALKNEAPVTTDGHRLTVMVNAGLRDDVAALD 465 Query: 561 ANGADGVGLLRTEFLFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYL 620 GADG+GL RTEF FL P + QR Y++VLDA G R V RT+D+GGDK L YL Sbjct: 466 LTGADGIGLFRTEFQFLVSATLPQRDSQRRLYKDVLDAAGDRPVTFRTVDIGGDKALPYL 525 Query: 621 PLPV---EENPALGLRGIHLGQARPELLDQQLRALLRVEPLERCRILLPMVSE---VDEL 674 EENPA+G R + L R L+ Q RALL ++ PMVSE DE Sbjct: 526 DHDENGEEENPAMGWRALRLALDREGLMKVQARALLEAAAGRTLNVMFPMVSEPWEFDEA 585 Query: 675 RAIRRRLGELATQLGIERLP---ELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQYAL 731 R + G +LP G M+EVP+ A + D L DFLS+GTNDL+Q+ Sbjct: 586 RTLFETQRAWLESRG-HKLPLHIRYGAMLEVPALAEVLDLLLPRLDFLSVGTNDLTQFLF 644 Query: 732 AMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGLGVE 791 A DR H LA R D L P++LR + + A AA + VCG + PL L+GLG++ Sbjct: 645 AADRAHPKLAVRYDWLSPSILRFLRRVTAEAAEADVPLAVCGEMGGRPLEAMALIGLGID 704 Query: 792 ELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARAVRD--ACLQHW 839 LS+ P VG IK VR LD A+ + +LD R +D A L+ W Sbjct: 705 RLSITPAAVGPIKAMVRSLDRAKLIAAMRGMLD----RPPQDMRAALEQW 750 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: 1356 Number of extensions: 68 Number of successful extensions: 5 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