GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Thauera aminoaromatica S2

Align N-acetyl-D-glucosamine kinase; GlcNAc kinase; EC 2.7.1.59 (characterized)
to candidate WP_004325323.1 C665_RS17905 ROK family protein

Query= SwissProt::Q8ZPZ9
         (303 letters)



>NCBI__GCF_000310185.1:WP_004325323.1
          Length = 301

 Score =  229 bits (584), Expect = 6e-65
 Identities = 125/296 (42%), Positives = 170/296 (57%), Gaps = 4/296 (1%)

Query: 4   GFDIGGTKIALGVFDSTRRLQWEKRVPTPHTSYSAFLDAVCELVEEADQRFGVKGSVGIG 63
           G D+GGTKI L V D+  R +W +RVPTP   Y   L A+  LVEEA++  G    +G+G
Sbjct: 6   GIDLGGTKIELVVLDADGRERWRRRVPTPQGDYGGTLRAIAALVEEAERLTGAGARIGVG 65

Query: 64  IPGMPETEDGTLYAANVPAASGKPLRADLSARLDRDVRLDNDANCFALSEAWDDEFTQYP 123
            PG P   DG +  AN    +G+PL+ DL A L R +RL NDANC A+SEA D       
Sbjct: 66  TPGSPSPRDGRIRNANSTCLNGQPLQQDLEALLRRPLRLANDANCLAMSEAADGAGAGAR 125

Query: 124 LVMGLILGTGVGGGLVLNGKPITGQSYITGEFGHMRLPVDALTLMGFDFPLRRCGCGQMG 183
            V   ILGTGVGGG+V++ K + G + + GE+GH  LP+ A      D PL  C CG+ G
Sbjct: 126 TVFAAILGTGVGGGIVVDQKLLVGANAVAGEWGHNPLPLPAPD----DLPLPACYCGRAG 181

Query: 184 CIENYLSGRGFAWLYQHYYDQSLQAPEIIALWEQGDEQAHAHVERYLDLLAVCLGNILTI 243
           CIE YLSG G A  +  +  + L A  I     +G   + A +ERY   LA  L  ++ +
Sbjct: 182 CIETYLSGPGLAADHLRHGGEPLDAAAIARQATEGQRASQASLERYELRLARALAGVINL 241

Query: 244 VDPDLLVIGGGLSNFTAITTQLAERLPRHLLPVARAPRIERARHGDAGGMRGAAFL 299
           +DP+++V+GGGLS    +   +  R   H+     + R+  ARHGDA G+RGAA+L
Sbjct: 242 LDPEVIVLGGGLSQIARLYEHVPRRWAAHVFSDTVSTRLLPARHGDASGVRGAAWL 297


Lambda     K      H
   0.322    0.142    0.441 

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: 292
Number of extensions: 17
Number of successful extensions: 2
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: 301
Length adjustment: 27
Effective length of query: 276
Effective length of database: 274
Effective search space:    75624
Effective search space used:    75624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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