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_RS16295 BWI76_RS16295 bifunctional PTS system maltose and glucose-specific transporter subunits IICB
Query= SwissProt::Q9S2H4 (416 letters) >FitnessBrowser__Koxy:BWI76_RS16295 Length = 530 Score = 224 bits (571), Expect = 5e-63 Identities = 145/423 (34%), Positives = 216/423 (51%), Gaps = 34/423 (8%) Query: 18 LFQGLQKVGRSLQLPIAVLPAAGIMVRLGQ-----DDIFGKDGLGWDKVAAVF---NNAG 69 L++ Q++G++ LP+A+L GIM+ +G D + L + AVF G Sbjct: 11 LWEFFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVLTLLPWLDVPLLQAVFIWMGKVG 70 Query: 70 GALTGSLPILFCIGVAIGFAKKADGSTALAAVVGFLVYSKVLEAF-------PVTEAVVQ 122 LP++FCI + +G A++ G A A VG+ V + + + P T+A V Sbjct: 71 SFAFSFLPVMFCIAIPLGLARENKGVAAFAGFVGYAVMNLAVNFWLTAKGILPTTDAAVL 130 Query: 123 DGADVAATYN----DPGVLGGIIMGLLAAVLWQRYHRKKLVDWLGFFNGRRLVPIIMAFV 178 ++ D G+LG +I G++ +L +R+H +L D L FF G R VPII V Sbjct: 131 KANNIQNIIGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIITTVV 190 Query: 179 GIVVGVFFGLVWEPIGDGISNFGEWMTGLGSGGAALFGGVNRALIPVGMHQF-VNTVAWF 237 +VG+ L+W GI+ G+ + G G +FG R L+P G+H V + + Sbjct: 191 LGLVGLVIPLIWPVFAMGINALGQVINSAGDFGPMIFGTGERLLLPFGLHHILVALIRFT 250 Query: 238 QLGDFTNSAGDVVHGDITRFLA----------GDPSAGIFQAGFFPIMMFGLPAAALAMA 287 + G + G V G +T F A + + G P + GLP AALAM Sbjct: 251 EAGGTMDVCGHSVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMY 310 Query: 288 HTARPERRKAVLGMMISLAATSFVTGVTEPIEFSFMFIAPVLYVLHAVLTAISMAITWGL 347 H ARPE R + G++IS V G TEP+EF F+F+APVLYV+HA+LT + + L Sbjct: 311 HCARPENRHKIKGLLISGVIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTMMAIL 370 Query: 348 GVHAGFNFSAGFID---YALNWHLATKPWLIIPIGLVFAAIYYVTFRFAIVKFNLKTPGR 404 GV G N ID + + L+TK +L+ + ++ A+YY FRFAI +FNLKTPGR Sbjct: 371 GVTIG-NTDGNVIDFVVFGILHGLSTKWYLVPVVAAIWFAVYYGIFRFAITRFNLKTPGR 429 Query: 405 EPE 407 + E Sbjct: 430 DIE 432 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: 642 Number of extensions: 43 Number of successful extensions: 6 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: 530 Length adjustment: 33 Effective length of query: 383 Effective length of database: 497 Effective search space: 190351 Effective search space used: 190351 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: 51 (24.3 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