GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Shewanella sp. ANA-3

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate 7025547 Shewana3_2698 N-acetylglucosamine kinase (RefSeq)

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



>FitnessBrowser__ANA3:7025547
          Length = 308

 Score =  185 bits (469), Expect = 1e-51
 Identities = 111/294 (37%), Positives = 165/294 (56%), Gaps = 4/294 (1%)

Query: 5   GIDLGGTKIELVTLNEKGEEVFRKRVPTP-KDYRATLEAVAGLVHDSEKETGQVSSVGIG 63
           G+D+GGTKIEL   + +     + R+ TP +DY A +  +A  +  ++++ G+  +VGI 
Sbjct: 4   GLDIGGTKIELAIFDTQLALQDKWRLSTPGQDYSAFMATLAEQIEKADQQCGERGTVGIA 63

Query: 64  IPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAGKT 123
           +PGVV A  G V +SN   LN + +  DL  +L R V I ND  CFA+SE+V G G G +
Sbjct: 64  LPGVVKA-DGTVISSNVPCLNQRRVAHDLAQLLNRTVAIGNDCRCFALSEAVLGVGRGYS 122

Query: 124 LVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLPWMTA--DEFNSTRCFCGNADCI 181
            V G ILGTG G G+ I+ K++ G N + GE+GH  +    A   +     C CG   C 
Sbjct: 123 RVLGMILGTGTGGGLCIDGKLYLGANRLAGEFGHQGVSANVACRHQLPLYVCGCGLEGCA 182

Query: 182 ETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVINLLD 241
           ET+VSGTG  R ++   G+ A     +  +   +PLA   F  ++D L   +A ++  +D
Sbjct: 183 ETYVSGTGLGRLYQDIAGQTADTFAWLNALRCNDPLAIKTFDTYMDILGSLMASLVLAMD 242

Query: 242 PDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWL 295
           PD+IVLGGG+S ++EI   LP     ++  G    +      G++SGVRGAA L
Sbjct: 243 PDIIVLGGGLSEVEEILAALPQATKAHLFDGVTLPQFKLADFGSASGVRGAALL 296


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: 310
Number of extensions: 17
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: 308
Length adjustment: 27
Effective length of query: 283
Effective length of database: 281
Effective search space:    79523
Effective search space used:    79523
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