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 H281DRAFT_01853 H281DRAFT_01853 PTS system D-glucose-specific IIB component, Glc family /PTS system D-glucose-specific IIC component, Glc family
Query= SwissProt::Q9S2H4 (416 letters) >FitnessBrowser__Burk376:H281DRAFT_01853 Length = 596 Score = 322 bits (824), Expect = 2e-92 Identities = 182/394 (46%), Positives = 244/394 (61%), Gaps = 11/394 (2%) Query: 19 FQGLQKVGRSLQLPIAVLPAAGIMVRLGQDDIFGKDGLGWDKVAAVFNNAGGALTGSLPI 78 F LQKVG+SL LP+AVLP AG+++ LG D G V A+ NAG + +LP+ Sbjct: 6 FGVLQKVGKSLMLPVAVLPVAGLLLGLGATDFHGYVPA---IVLALMKNAGDVIFANLPL 62 Query: 79 LFCIGVAIGFAKKADGSTALAAVVGFLVYSKVLEAFPVTEAVVQDGADVAATYNDPGVLG 138 +F IGVA+GF + DG + +AA +G+LV + L E + D + GV G Sbjct: 63 IFAIGVALGFTEN-DGVSGIAATIGYLVMTATLGVIAKVEGIEPDMI-MGIPSIQTGVFG 120 Query: 139 GIIMGLLAAVLWQRYHRKKLVDWLGFFNGRRLVPIIMAFVGIVVGVFFGLVWEPIGDGIS 198 GI+ G LAA ++ RY+R L +LGFF G+R VPI+ A IV+G +VW PIG I Sbjct: 121 GILAGGLAAWMFNRYYRIALPAYLGFFAGKRFVPIVTAIGSIVLGAILSVVWPPIGSAIK 180 Query: 199 NFGEWMTGLGSGGAA-LFGGVNRALIPVGMHQFVNTVAWFQLGDFTN-SAGDVVHGDITR 256 F +W AA ++G V R LIP G+H N +F+ G F + + G VVHGDITR Sbjct: 181 AFSQWAAVSDPRTAATVYGFVERLLIPFGLHHIWNVPFFFEAGSFLDPTTGKVVHGDITR 240 Query: 257 FLAGDPSAGIFQAGFFPIMMFGLPAAALAMAHTARPERRKAVLGMMISLAATSFVTGVTE 316 F AGD +AGI AG F MFGLPAAA+A+ H A+PE + AV GMM+S A TSF+TG+TE Sbjct: 241 FFAGDRTAGIL-AGAFLFKMFGLPAAAIAIWHCAKPENKVAVGGMMVSAALTSFLTGITE 299 Query: 317 PIEFSFMFIAPVLYVLHAVLTAISMAITWGLGVHAGFNFSAGFIDYA---LNWHLATKPW 373 PIEF+F+F+APVLY++HA L A + + LG+ GF FS G ID+ L + +T W Sbjct: 300 PIEFAFLFVAPVLYLIHACLAASAQFVANTLGMRMGFTFSQGGIDFLMFNLIGNKSTHAW 359 Query: 374 LIIPIGLVFAAIYYVTFRFAIVKFNLKTPGREPE 407 + +G ++A IYY FRF I +F+LKTPGRE + Sbjct: 360 YVFILGPIYAVIYYGVFRFVITRFDLKTPGREDD 393 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: 672 Number of extensions: 32 Number of successful extensions: 8 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: 596 Length adjustment: 34 Effective length of query: 382 Effective length of database: 562 Effective search space: 214684 Effective search space used: 214684 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