Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)
Query= reanno::BFirm:BPHYT_RS02745 (591 letters) >FitnessBrowser__MR1:200788 Length = 499 Score = 274 bits (700), Expect = 7e-78 Identities = 169/473 (35%), Positives = 253/473 (53%), Gaps = 40/473 (8%) Query: 10 QRLGRALMLPIAVLPVAGLLLRLG------QPDVFNIKMIADAGGAIFDNLPLLFAIGVA 63 QRL +AL++PIA+LP AG++L L P+V N+ M+A G IF +P+LFA+ VA Sbjct: 29 QRLSQALLIPIAILPAAGVMLGLTVSPIPFMPEVLNVLMLA-VGKLIFAIMPILFAVAVA 87 Query: 64 VGFAKDNNGVAGLAGAIGYLIEVAVMKDIND-------------KLNMGVLSGIVAGIVA 110 +GF +D G+A GY + A + + D L+ G+ G++ G V Sbjct: 88 IGFCRDQ-GIAAFTAVFGYGVMTATLAALADLYQLPTQLVLGMETLDTGIAGGMLIGGVT 146 Query: 111 GLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTT 170 + I+LP +FF G+R ++ + + LG ++W + +I+ W Sbjct: 147 CFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYVLAHIWPSLSLLIERVSDWAVY 206 Query: 171 AGALGAF-VFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFAGDPTAG 229 AF V+G L RLL+ GLHHI N+ + G + V G++ R+ AGDP AG Sbjct: 207 QKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQDAEVVRGEVARYLAGDPQAG 266 Query: 230 TFMTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFL 289 G+ + M+GLPAA LA++ A R V G++ S A S+LTGVTEPIEF+FMF+ Sbjct: 267 NLAGGYL-IKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFV 325 Query: 290 APVLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPIGLVYMVV 349 AP+L++IH +L+G++ +C L IH FS G +D+ L + LS W +G + V+ Sbjct: 326 APLLFLIHVMLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFAVLGPLTAVI 385 Query: 350 YYGLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASN 409 YY LFR I FN+ TPGR + S G + + IAALGG N Sbjct: 386 YYILFRGSILAFNLKTPGR--------LQSDGTKG--------SKESLRAIIAALGGRDN 429 Query: 410 LSVVDACTTRLRLSVVDSNKVSENELKTIGARGVLKRGSTNVQVIIGPEADII 462 + ++AC TRLRLSV V++ L +GA+GV+ G VQ++ G +A+ + Sbjct: 430 IVELNACLTRLRLSVHSPELVNKVRLSQLGAKGVIVMGK-GVQIVYGTKAETL 481 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: 833 Number of extensions: 44 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: 591 Length of database: 499 Length adjustment: 35 Effective length of query: 556 Effective length of database: 464 Effective search space: 257984 Effective search space used: 257984 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: 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