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 BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC
Query= SwissProt::Q9S2H4 (416 letters) >FitnessBrowser__Koxy:BWI76_RS08220 Length = 650 Score = 367 bits (941), Expect = e-106 Identities = 190/394 (48%), Positives = 262/394 (66%), Gaps = 28/394 (7%) Query: 23 QKVGRSLQLPIAVLPAAGIMVRLGQDDIFGKDGLGWDKVAAVFNNAGGALTGSLPILFCI 82 Q++GR+LQLPIAVLP A +++R GQ D+ + AGGA+ +L ++F I Sbjct: 8 QRLGRALQLPIAVLPVAALLLRFGQPDLLN---------ISFIAQAGGAIFDNLALIFAI 58 Query: 83 GVAIGFAKKADGSTALAAVVGFLVYSKVLEAFPVTEAVVQDGADVAATYNDPGVLGGIIM 142 GVA ++K + G+ ALA VG+ V +K + + A+ + GVL GII Sbjct: 59 GVASSWSKDSAGAAALAGAVGYFVLTKAMVT--INPAI------------NMGVLAGIIT 104 Query: 143 GLLAAVLWQRYHRKKLVDWLGFFNGRRLVPIIMAFVGIVVGVFFGLVWEPIGDGISNFGE 202 GL+ ++ R+ KL D+L FF G+R VPI F +V+ FG VW P+ + I GE Sbjct: 105 GLVGGAVYNRWSGIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQNAIHAGGE 164 Query: 203 WMTGLGSGGAALFGGVNRALIPVGMHQFVNTVAWFQLGDFTNSAGDVVHGDITRFLAGDP 262 W+ G G+ G+ +FG +NR LIP G+HQ +NT+AWFQ+G+FTN+AG V HGDI RF AGD Sbjct: 165 WIVGAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGAVFHGDINRFYAGDG 224 Query: 263 SAGIFQAGFFPIMMFGLPAAALAMAHTARPERRKAVLGMMISLAATSFVTGVTEPIEFSF 322 +AG+F +GFFPIMMFGLP AALAM A ERR V GM++S+A T+F+TGVTEP+EF F Sbjct: 225 TAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAITAFLTGVTEPLEFLF 284 Query: 323 MFIAPVLYVLHAVLTAISMAITWGLGVHAGFNFSAGFIDYALNWHL---ATKPWLIIPIG 379 MF+AP+LY+LHA+LT IS+ + LG+HAGF+FSAG IDY L + L + W++I +G Sbjct: 285 MFLAPLLYLLHAILTGISLFVATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLIVMG 344 Query: 380 LVFAAIYYVTFRFAIVKFNLKTPGREPEEEVEDL 413 +VF IY++ F I FNLKTPGR E++V+D+ Sbjct: 345 VVFFVIYFLLFSAVIRMFNLKTPGR--EDKVDDV 376 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: 779 Number of extensions: 39 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: 650 Length adjustment: 35 Effective length of query: 381 Effective length of database: 615 Effective search space: 234315 Effective search space used: 234315 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