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 BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC
Query= SwissProt::Q9S2H4 (416 letters) >FitnessBrowser__BFirm:BPHYT_RS02745 Length = 591 Score = 389 bits (998), Expect = e-112 Identities = 200/396 (50%), Positives = 264/396 (66%), Gaps = 26/396 (6%) Query: 19 FQGLQKVGRSLQLPIAVLPAAGIMVRLGQDDIFGKDGLGWDKVAAVFNNAGGALTGSLPI 78 F +Q++GR+L LPIAVLP AG+++RLGQ D+F + +AGGA+ +LP+ Sbjct: 6 FLKIQRLGRALMLPIAVLPVAGLLLRLGQPDVFN---------IKMIADAGGAIFDNLPL 56 Query: 79 LFCIGVAIGFAKKADGSTALAAVVGFLVYSKVLEAFPVTEAVVQDGADVAATYNDPGVLG 138 LF IGVA+GFAK +G LA +G+L+ V++ D+ N GVL Sbjct: 57 LFAIGVAVGFAKDNNGVAGLAGAIGYLIEVAVMK-------------DINDKLN-MGVLS 102 Query: 139 GIIMGLLAAVLWQRYHRKKLVDWLGFFNGRRLVPIIMAFVGIVVGVFFGLVWEPIGDGIS 198 GI+ G++A +L+ RY KL D+L FF G+R VPI+ V +V+G+ FG VW+P+ I Sbjct: 103 GIVAGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVID 162 Query: 199 NFGEWMTGLGSGGAALFGGVNRALIPVGMHQFVNTVAWFQLGDFTNSAGDVVHGDITRFL 258 G W+T G+ GA +FG +NR L+ G+H +N++ WF G FT G V GD+ RF Sbjct: 163 TAGHWLTTAGALGAFVFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFF 222 Query: 259 AGDPSAGIFQAGFFPIMMFGLPAAALAMAHTARPERRKAVLGMMISLAATSFVTGVTEPI 318 AGDP+AG F GFFP+MMFGLPAA LAM H A ERR V G++ S+A TSF+TGVTEPI Sbjct: 223 AGDPTAGTFMTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPI 282 Query: 319 EFSFMFIAPVLYVLHAVLTAISMAITWGLGVHAGFNFSAGFIDYALNWHLATKPWLIIPI 378 EFSFMF+APVLYV+HA+LT IS+AI LG+H GF FSAG IDY LN+ L+T+ W IPI Sbjct: 283 EFSFMFLAPVLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPI 342 Query: 379 GLVFAAIYYVTFRFAIVKFNLKTPGREP---EEEVE 411 GLV+ +YY FRF I KFN+ TPGREP +E+V+ Sbjct: 343 GLVYMVVYYGLFRFFIRKFNMATPGREPAAADEQVD 378 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: 740 Number of extensions: 39 Number of successful extensions: 3 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: 591 Length adjustment: 34 Effective length of query: 382 Effective length of database: 557 Effective search space: 212774 Effective search space used: 212774 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