GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Klebsiella michiganensis M5al

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate BWI76_RS11225 BWI76_RS11225 N-acetylglucosamine kinase

Query= reanno::SB2B:6937235
         (310 letters)



>FitnessBrowser__Koxy:BWI76_RS11225
          Length = 303

 Score =  204 bits (518), Expect = 3e-57
 Identities = 118/296 (39%), Positives = 172/296 (58%), Gaps = 5/296 (1%)

Query: 5   GIDLGGTKIELVTLNEKGEEVFRKRVPTPKD-YRATLEAVAGLVHDSEKETGQVSSVGIG 63
           G D+GG+KI L   ++     + KRV TPK+ Y A L+AV  LV ++++  G   SVGIG
Sbjct: 4   GFDIGGSKIALGIFDKARRLQWEKRVATPKESYEAFLQAVEALVQEADQRFGCQGSVGIG 63

Query: 64  IPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAGKT 123
           IPG+     G +  +N    +G+ +  DL   LGR+VR+ NDANCFA+SE+ D       
Sbjct: 64  IPGMPETEDGTLYAANVPAASGRRLRADLSERLGRDVRLDNDANCFALSEAWDDEFTQYP 123

Query: 124 LVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLP----WMTADEFNSTRCFCGNAD 179
           LV G ILGTG G G+ +N K   G   I GE+GH  LP     +   +F  TRC CG   
Sbjct: 124 LVMGLILGTGVGGGLVLNGKSITGHRYITGEFGHIRLPVDALEVVGRDFPLTRCGCGQLG 183

Query: 180 CIETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVINL 239
           CIE ++SG GF   ++    ++ +  EIVAL  +G+  A     R++D LA  L +++ +
Sbjct: 184 CIENYLSGRGFAWLYQHFYQQSLTSPEIVALWQQGDAKAREHVERYLDLLAVCLGNILTI 243

Query: 240 LDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWL 295
           +DPD++VLGGG+SN   I E L   LP+++L      ++ +  HG + G+RGAA+L
Sbjct: 244 VDPDLLVLGGGLSNFTAITEGLAQRLPRHLLPVASVPRIERARHGDAGGMRGAAFL 299


Lambda     K      H
   0.318    0.138    0.424 

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: 259
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: 310
Length of database: 303
Length adjustment: 27
Effective length of query: 283
Effective length of database: 276
Effective search space:    78108
Effective search space used:    78108
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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