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 14809 b0679 fused N-acetyl glucosamine specific PTS enzyme: IIC, IIB , and IIA components (NCBI)
Query= SwissProt::Q9S2H4 (416 letters) >FitnessBrowser__Keio:14809 Length = 648 Score = 370 bits (950), Expect = e-107 Identities = 191/390 (48%), Positives = 261/390 (66%), Gaps = 26/390 (6%) Query: 23 QKVGRSLQLPIAVLPAAGIMVRLGQDDIFGKDGLGWDKVAAVFNNAGGALTGSLPILFCI 82 Q++GR+LQLPIAVLP A +++R GQ D+ A AGGA+ +L ++F I Sbjct: 8 QRLGRALQLPIAVLPVAALLLRFGQPDLLN---------VAFIAQAGGAIFDNLALIFAI 58 Query: 83 GVAIGFAKKADGSTALAAVVGFLVYSKVLEAFPVTEAVVQDGADVAATYNDPGVLGGIIM 142 GVA ++K + G+ ALA VG+ V +T+A+V ++ + GVL GII Sbjct: 59 GVASSWSKDSAGAAALAGAVGYFV---------LTKAMVTINPEI-----NMGVLAGIIT 104 Query: 143 GLLAAVLWQRYHRKKLVDWLGFFNGRRLVPIIMAFVGIVVGVFFGLVWEPIGDGISNFGE 202 GL+ + R+ KL D+L FF G+R VPI F +V+ FG VW P+ I GE Sbjct: 105 GLVGGAAYNRWSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGE 164 Query: 203 WMTGLGSGGAALFGGVNRALIPVGMHQFVNTVAWFQLGDFTNSAGDVVHGDITRFLAGDP 262 W+ G+ G+ +FG +NR LIP G+HQ +NT+AWFQ+G+FTN+AG V HGDI RF AGD Sbjct: 165 WIVSAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDG 224 Query: 263 SAGIFQAGFFPIMMFGLPAAALAMAHTARPERRKAVLGMMISLAATSFVTGVTEPIEFSF 322 +AG+F +GFFPIMMFGLP AALAM A ERR V GM++S+A T+F+TGVTEP+EF F Sbjct: 225 TAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLF 284 Query: 323 MFIAPVLYVLHAVLTAISMAITWGLGVHAGFNFSAGFIDYALNWHL---ATKPWLIIPIG 379 MF+AP+LY+LHA+LT IS+ + LG+HAGF+FSAG IDYAL ++L + W+++ +G Sbjct: 285 MFLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMG 344 Query: 380 LVFAAIYYVTFRFAIVKFNLKTPGREPEEE 409 ++F AIY+V F I FNLKTPGRE +E+ Sbjct: 345 VIFFAIYFVVFSLVIRMFNLKTPGREDKED 374 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: 760 Number of extensions: 40 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: 648 Length adjustment: 35 Effective length of query: 381 Effective length of database: 613 Effective search space: 233553 Effective search space used: 233553 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