Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC
Query= BRENDA::P09323 (648 letters) >FitnessBrowser__BFirm:BPHYT_RS02745 Length = 591 Score = 543 bits (1398), Expect = e-158 Identities = 275/506 (54%), Positives = 348/506 (68%), Gaps = 12/506 (2%) Query: 8 QRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGVASSWSKD 67 QRLGRAL LPIAVLPVA LLLR GQPD+ N+ IA AGGAIFDNL L+FAIGVA ++KD Sbjct: 10 QRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAIGVAVGFAKD 69 Query: 68 SAGAAALAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAAYNRWSDIKLPDFLSFF 127 + G A LAGA+GY + M IN ++NMGVL+GI+ G+V G YNR+ DIKLPD+L+FF Sbjct: 70 NNGVAGLAGAIGYLIEVAVMKDINDKLNMGVLSGIVAGIVAGLLYNRYKDIKLPDYLAFF 129 Query: 128 GGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFINRLLIPT 187 GGKRFVPI TG CLVL FGYVW PVQ I G W+ +AGALG+ +FG +NRLL+ T Sbjct: 130 GGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTTAGALGAFVFGVLNRLLLVT 189 Query: 188 GLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLPGAALA 247 GLH +LN++ WF G FT G GD++RF+AGD TAG FM+GFFP+MMFGLP A LA Sbjct: 190 GLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFAGDPTAGTFMTGFFPVMMFGLPAACLA 249 Query: 248 MYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLFVAT 307 M+ APKERR +VGG+L S+A+T+FLTGVTEP+EF FMFLAP+LY++HALLTGISL + + Sbjct: 250 MFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALLTGISLAICS 309 Query: 308 LLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKTP 367 LGIH GF+FSAGAIDY L Y L S W + +G+++ +Y+ +F IR FN+ TP Sbjct: 310 ALGIHLGFTFSAGAIDYVLNYGL---STRGWWAIPIGLVYMVVYYGLFRFFIRKFNMATP 366 Query: 368 GRE-----DKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVAD 422 GRE ++ D S A YIAA+GG NL +DAC TRLRL+V D Sbjct: 367 GREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLSVVDACTTRLRLSVVD 426 Query: 423 SARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAMKKVVARGPVAAASAEATPAT 482 S +V++ K +GA GV+K +QVI+G +A+ I D ++ V+A+G A PA Sbjct: 427 SNKVSENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIRTVIAQGGGDAVK----PAA 482 Query: 483 AAPVAKPQAVPNAVSIAELVSPITGD 508 AAP A P A S+A+ P+ D Sbjct: 483 AAPAQVVAAAPVAASVAQGSGPLDPD 508 Lambda K H 0.324 0.139 0.408 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: 1092 Number of extensions: 63 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: 648 Length of database: 591 Length adjustment: 37 Effective length of query: 611 Effective length of database: 554 Effective search space: 338494 Effective search space used: 338494 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: 41 (22.0 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