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 PfGW456L13_4833 PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)
Query= SwissProt::Q9S2H4 (416 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4833 Length = 571 Score = 372 bits (954), Expect = e-107 Identities = 187/398 (46%), Positives = 260/398 (65%), Gaps = 24/398 (6%) Query: 20 QGLQKVGRSLQLPIAVLPAAGIMVRLGQDDIFGKDGLGWDKVAAVFNNAGGALTGSLPIL 79 +GLQ++GR+L LPIA+LP AG+++RLG D+ A+ ++AG + +L ++ Sbjct: 7 EGLQRLGRALMLPIAILPIAGLLLRLGDTDLLN---------IAIIHDAGQVIFANLAMI 57 Query: 80 FCIGVAIGFAKKADGSTALAAVVGFLVYSKVLEAFPVTEAVVQDGADVAATYNDPGVLGG 139 F IG+A+GFA+ +G+ LA V+G+LV L+A + + G+L G Sbjct: 58 FAIGIAVGFARDNNGTAGLAGVIGYLVMISTLKALDPSINM--------------GMLAG 103 Query: 140 IIMGLLAAVLWQRYHRKKLVDWLGFFNGRRLVPIIMAFVGIVVGVFFGLVWEPIGDGISN 199 I+ GL+A L+ R+ KL ++L FF GRR VPI+ F + +GV FG +W PI GI++ Sbjct: 104 IVSGLMAGALYNRFKDIKLPEYLAFFGGRRFVPIVTGFAAVGLGVVFGYIWPPIQHGINS 163 Query: 200 FGEWMTGLGSGGAALFGGVNRALIPVGMHQFVNTVAWFQLGDFTN-SAGDVVHGDITRFL 258 FG M GS GA +FG NR LI G+H +N +AWF G+FT+ + G +V GD++R+ Sbjct: 164 FGTLMMESGSFGAFVFGLFNRLLIVTGLHHILNNMAWFVFGNFTDPTTGALVTGDLSRYF 223 Query: 259 AGDPSAGIFQAGFFPIMMFGLPAAALAMAHTARPERRKAVLGMMISLAATSFVTGVTEPI 318 AGDP G F G FP+M+FGLPAA LAM A P RRK + G+ +S+A T+F+TGVTEPI Sbjct: 224 AGDPKGGQFMTGMFPMMIFGLPAACLAMYRNALPARRKVMGGIFLSMALTAFLTGVTEPI 283 Query: 319 EFSFMFIAPVLYVLHAVLTAISMAITWGLGVHAGFNFSAGFIDYALNWHLATKPWLIIPI 378 EF+FMF+AP+L+VLHA+LT +SMAIT L +H GF FS GFID L W +T WL+ P+ Sbjct: 284 EFAFMFLAPLLFVLHALLTGLSMAITNALNIHLGFTFSGGFIDMILGWGKSTNGWLVFPV 343 Query: 379 GLVFAAIYYVTFRFAIVKFNLKTPGREPEEEVEDLTKA 416 GL +A IYYV F F I +F+LKTPGRE +VE + A Sbjct: 344 GLAYAVIYYVVFDFCIRRFDLKTPGRETSADVEQVAVA 381 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: 679 Number of extensions: 36 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: 571 Length adjustment: 34 Effective length of query: 382 Effective length of database: 537 Effective search space: 205134 Effective search space used: 205134 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: 52 (24.6 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