Align PTS system N-acetylglucosamine-specific EIIC component; PTS system GlcNAc-specific EIIC component; GlcNAc-specific transporter; N-acetylglucosamine permease IIC component; GlcNAc permease IIC component (characterized)
to candidate WP_091292425.1 BLV57_RS24320 PTS transporter subunit EIIC
Query= SwissProt::Q9S2H4 (416 letters) >NCBI__GCF_900107045.1:WP_091292425.1 Length = 409 Score = 395 bits (1015), Expect = e-114 Identities = 210/417 (50%), Positives = 278/417 (66%), Gaps = 17/417 (4%) Query: 3 TATDTAAPAKKRGSGLFQGLQKVGRSLQLPIAVLPAAGIMVRLGQDDIFGKDGLGWDKVA 62 +AT A + RG GLQ+ GRSL LPIA LPAAGI++RLGQ+D+ G GLGWDKVA Sbjct: 2 SATTAAGKGQSRG---LAGLQRFGRSLMLPIAALPAAGILLRLGQEDLLGPKGLGWDKVA 58 Query: 63 AVFNNAGGALTGSLPILFCIGVAIGFAKKADGSTALAAVVGFLVYSKVLEAFPVTEAV-- 120 VF AGG L LP+LF + +A+GFA+K DGSTA+AAVVG++V++ V++ F ++V Sbjct: 59 DVFAAAGGGLFDWLPLLFAVAIAVGFARKGDGSTAVAAVVGWIVFNHVVQVFAPIKSVEG 118 Query: 121 VQDGADVAATYNDPGVLGGIIMGLLAAVLWQRYHRKKLVDWLGFFNGRRLVPIIMAFVGI 180 ++G +A VLGG+++GL+AA+LWQ+YHR KL +L FF GRR VPII +FV I Sbjct: 119 FKEGWYLAPIKWPYSVLGGVVVGLVAALLWQKYHRIKLPAYLAFFGGRRFVPIITSFVMI 178 Query: 181 VVGVFFGLVWEPIGDGISNFGEWMTGLGSGGAALFGGVNRALIPVGMHQFVNTVAWFQLG 240 ++GV FGL+++ + I GE T G ++G +NR LIP+G+HQ +N WF Sbjct: 179 ILGVLFGLIFKQVDHVIHWVGEQATANSVVGGGVYGLLNRLLIPIGLHQLLNVPVWFIFD 238 Query: 241 DFTNSAGDVVHGDITRFLAGDPSAGIFQAGFFPIMMFGLPAAALAMAHTARPERRKAVLG 300 GD+ F +G F GFFPI MF LPAAALA+ TA+P ++K V G Sbjct: 239 G----------GDLNNFFNHVQGSGSFMTGFFPIFMFALPAAALAIWQTAKPSQKKVVGG 288 Query: 301 MMISLAATSFVTGVTEPIEFSFMFIAPVLYVLHAVLTAISMAITWGLGVHAGFNFSAGFI 360 +MI+ A TSF+TGVTEPIEF+FMF+A LY+ HAV+T +SM + LG+ GF+FSAG I Sbjct: 289 VMIAAALTSFLTGVTEPIEFAFMFVAWPLYLFHAVMTGLSMVLVNALGIKLGFSFSAGAI 348 Query: 361 DYALNWHL--ATKPWLIIPIGLVFAAIYYVTFRFAIVKFNLKTPGREPEEEVEDLTK 415 D+A N L A K W++IPIGLVFA IY+ F+F I K+NL TPGRE + DL K Sbjct: 349 DFAFNSSLDTANKAWMLIPIGLVFAVIYFFVFKFVITKWNLATPGREDDSIEADLEK 405 Lambda K H 0.326 0.142 0.440 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: 640 Number of extensions: 46 Number of successful extensions: 4 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: 416 Length of database: 409 Length adjustment: 31 Effective length of query: 385 Effective length of database: 378 Effective search space: 145530 Effective search space used: 145530 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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