Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC
Query= reanno::BFirm:BPHYT_RS02745 (591 letters) >FitnessBrowser__Koxy:BWI76_RS08220 Length = 650 Score = 541 bits (1395), Expect = e-158 Identities = 279/494 (56%), Positives = 347/494 (70%), Gaps = 15/494 (3%) Query: 10 QRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAIGVAVGFAKD 69 QRLGRAL LPIAVLPVA LLLR GQPD+ NI IA AGGAIFDNL L+FAIGVA ++KD Sbjct: 8 QRLGRALQLPIAVLPVAALLLRFGQPDLLNISFIAQAGGAIFDNLALIFAIGVASSWSKD 67 Query: 70 NNGVAGLAGAIGYLIEVAVMKDINDKLNMGVLSGIVAGIVAGLLYNRYKDIKLPDYLAFF 129 + G A LAGA+GY + M IN +NMGVL+GI+ G+V G +YNR+ IKLPD+L+FF Sbjct: 68 SAGAAALAGAVGYFVLTKAMVTINPAINMGVLAGIITGLVGGAVYNRWSGIKLPDFLSFF 127 Query: 130 GGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTTAGALGAFVFGVLNRLLLVT 189 GGKRFVPI TG CLVL FGYVW PVQ I G W+ AGALG+ +FG +NRLL+ T Sbjct: 128 GGKRFVPIATGFFCLVLAAIFGYVWPPVQNAIHAGGEWIVGAGALGSGIFGFINRLLIPT 187 Query: 190 GLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFAGDPTAGTFMTGFFPVMMFGLPAACLA 249 GLH +LN++ WF G FT GA GD++RF+AGD TAG FM+GFFP+MMFGLP A LA Sbjct: 188 GLHQVLNTIAWFQIGEFTNAAGAVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLPGAALA 247 Query: 250 MFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALLTGISLAICS 309 M+ APKERR +VGG+L S+A+T+FLTGVTEP+EF FMFLAP+LY++HA+LTGISL + + Sbjct: 248 MYFAAPKERRPMVGGMLLSVAITAFLTGVTEPLEFLFMFLAPLLYLLHAILTGISLFVAT 307 Query: 310 ALGIHLGFTFSAGAIDYVLNYGL---STRGWWAIPIGLVYMVVYYGLFRFFIRKFNMATP 366 ALGIH GF+FSAGAIDYVL Y L S W I +G+V+ V+Y+ LF IR FN+ TP Sbjct: 308 ALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLIVMGVVFFVIYFLLFSAVIRMFNLKTP 367 Query: 367 GREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLSVVDACTTRLRLSVVD 426 GRE ++VD S A YIAA+GG NL +DAC TRLRL+V D Sbjct: 368 GRE-----DKVDDVVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVAD 422 Query: 427 SNKVSENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIRTVIAQGGGDAVKPAAAAPA 486 S V++ K +GA GV+K +QVI+G +A+ + DE++ V+A+G P AAA A Sbjct: 423 SALVNDAACKRLGASGVVKLNKQTIQVIVGAKAESVGDEMKKVVARG------PVAAA-A 475 Query: 487 QVVAAAPVAASVAQ 500 +APVAA + Sbjct: 476 AASHSAPVAAQAVK 489 Lambda K H 0.325 0.141 0.426 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: 1225 Number of extensions: 73 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: 591 Length of database: 650 Length adjustment: 37 Effective length of query: 554 Effective length of database: 613 Effective search space: 339602 Effective search space used: 339602 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 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