Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59 (characterized)
to candidate AZOBR_RS11685 AZOBR_RS11685 hypothetical protein
Query= CharProtDB::CH_002679 (303 letters) >FitnessBrowser__azobra:AZOBR_RS11685 Length = 299 Score = 212 bits (539), Expect = 1e-59 Identities = 127/300 (42%), Positives = 168/300 (56%), Gaps = 6/300 (2%) Query: 1 MYYGFDIGGTKIALGVFDSGRQLQWEKRVPTPRDSYDAFLDAVCELVAEADQRFGCK-GS 59 M G D+GGTKIA + + R TPR Y L A+ VA ++R G + + Sbjct: 1 MRIGVDLGGTKIAATLLAPDGTERARHRADTPR-GYAETLQALAGAVAALEERAGRRDAT 59 Query: 60 VGIGIPGMPETEDGTLYAANVPAASGKPLRADLSARLDRDVRLDNDANCFALSEAWDDEF 119 VG+ +PG+ + GT+ A N+P G+P ADL+ LDR VR+ NDAN F LSEA D Sbjct: 60 VGLCLPGIVDAAAGTVRAVNLPWLDGRPFAADLARALDRPVRIANDANAFVLSEAMDGAA 119 Query: 120 TQYPLVMGLILGTGVGGGLIFNGKPITGKSYITGEFGHMRLPVDALTMMGLDFPLRRCGC 179 PLV G+ILGTGVGGG++ + + + G + + GE+GH LP D P CGC Sbjct: 120 AGAPLVFGIILGTGVGGGIVADRRILPGANALAGEWGHNPLPWRVTE----DGPPVPCGC 175 Query: 180 GQHGCIENYLSGRGFAWLYQHYYHQPLQAPEIIALYDQGDEQARAHVERYLDLLAVCLGN 239 G+ GCIE L G G A L+ + L PEI A GD ARA ++R+ D LA L Sbjct: 176 GREGCIETLLCGAGLARLHLWRTGETLTPPEIAARAQSGDAPARATLDRHADALARALAA 235 Query: 240 ILTIVDPDLVVIGGGLSNFPAITTQLADRLPRHLLPVARVPRIERARHGDAGGMRGAAFL 299 ++ ++DPD+VV+GGGLS P + + R R L A R RARHG GMRGAA+L Sbjct: 236 VVNLLDPDVVVVGGGLSELPGLYEAVPARWGRWALSPAPRTRFLRARHGAESGMRGAAWL 295 Lambda K H 0.323 0.143 0.451 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: 281 Number of extensions: 14 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: 303 Length of database: 299 Length adjustment: 27 Effective length of query: 276 Effective length of database: 272 Effective search space: 75072 Effective search space used: 75072 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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