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 WP_012050679.1 SWIT_RS22755 phosphoenolpyruvate--protein phosphotransferase
Query= TCDB::Q9HXN5 (842 letters) >NCBI__GCF_000016765.1:WP_012050679.1 Length = 759 Score = 280 bits (715), Expect = 3e-79 Identities = 212/635 (33%), Positives = 302/635 (47%), Gaps = 35/635 (5%) Query: 209 FAG-QVASVDSLVGIMGLGVAEQ---DEVEVICRGEDSEAALGALLAALASATAGAPKDA 264 FAG + + VG++ + +Q D+VE+ AL + LA AGA Sbjct: 117 FAGVPIVRRERAVGVLAVQHRDQRRFDDVEI--------EALQTVAMVLAELIAGAGLID 168 Query: 265 PRAIAPGEPARPAAVAGTLAGVCASPGLASG-PLARLGAISLPADDGRHRPEEQHLALDQ 323 PG A LAG+ G+A G + I + E+H + Sbjct: 169 EGV--PGSKGTRDNGAVRLAGLKLVEGMARGRAVYHQPRIEIEHTVAEDIEVERHRVIS- 225 Query: 324 ALQRVRDDVQGSLQQARLGGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHR 383 A ++RD ++ ++A G + + + D G + + ID G+ A A R Sbjct: 226 AFSKMRDQIERMTREADFGAGGEHQDVLAMYKMFAYDEGWIRRINEAIDSGLTAEAAIER 285 Query: 384 AIQAQCEILQALGNLLLAERANDLRDLEKRVLRVL---LGDTAPLRVPAGAIVAAREITP 440 Q ++ +G+ LLA+R +DL DL R+LR++ LG A L + +I+ AR + P Sbjct: 286 VQQRTRMRMREIGDPLLADRMHDLEDLSNRLLRIVSGQLGTAAQLGLRHDSILIARNLGP 345 Query: 441 SDLAPLVDAGAAGLCMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQG 500 ++L G+ + EG T+HV I+AR+ G+P L + + EG ++LD G Sbjct: 346 AELLEYDRRRLKGVVLEEGSLTAHVTIVARAMGVPVLGRVKDVRRMIGEGDTLLLDGTAG 405 Query: 501 RLELSPDARRLEQVALQVAQREEQRRRQQADAQRE--ALTRDGRRIEIGANVASPREAAE 558 + + +A E A + Q+RR + A R+ A TRD RIE+ N + A Sbjct: 406 SVVVRANATMEE--AFEAKMMVGQKRRAEFAAMRDLPARTRDDLRIELMVNAGLRDDMAA 463 Query: 559 AFANGADGVGLLRTEFLFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLD 618 GADG+GL RTEF FL P E Q Y++VLDA G R VI RT+D+GGDK L Sbjct: 464 LDVTGADGIGLFRTEFQFLVSATLPQRERQLRLYRDVLDAAGDRPVIFRTVDIGGDKALP 523 Query: 619 YLPL---PVEENPALGLRGIHLGQARPELLDQQLRALLRVEPLERCRILLPMVSEVDELR 675 YL EENPALG R I LG R L+ Q RAL+ ++ PMVSE E Sbjct: 524 YLKAGDDADEENPALGWRAIRLGLERDALMKVQARALIEAAAGRTLNVMFPMVSEPWEFE 583 Query: 676 -------AIRRRLGELATQLGIERLPELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQ 728 A R+ + + G+ G M+EVP+ A D L DFLSIGTNDL+Q Sbjct: 584 EAVALFDAQRKWIHDHGR--GVPNAIRYGTMLEVPALAESLDMLLPRLDFLSIGTNDLTQ 641 Query: 729 YALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGL 788 + A DR + LA+R D L PA+LR I + G +GVCG + PL L+GL Sbjct: 642 FLFAADRANPKLAERYDWLSPAILRFIGRVTRQTRAAGVPIGVCGEMGGRPLEAMALIGL 701 Query: 789 GVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALL 823 G++ LS+ P VG +K +R LDA R L Sbjct: 702 GIDRLSITPAAVGPVKAMIRSLDAKALREAMDGFL 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: 1394 Number of extensions: 84 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 Apr 09 2024. 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