GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguK in Lactobacillus shenzhenensis LY-73

Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate WP_022529572.1 L248_RS07595 sugar kinase

Query= metacyc::MONOMER-12748
         (320 letters)



>NCBI__GCF_000469325.1:WP_022529572.1
          Length = 318

 Score =  228 bits (582), Expect = 1e-64
 Identities = 133/308 (43%), Positives = 183/308 (59%), Gaps = 6/308 (1%)

Query: 5   DILSFGETMAMFVAEH-GGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSL 63
           + L+ GE +A+F +E     L    HFHK +AGA+ NVA+G++RLG    +++R+G D  
Sbjct: 3   EFLTIGEPIALFASEDMDKSLKDAVHFHKFLAGAEVNVAVGVSRLGHSAQYITRLGEDPF 62

Query: 64  GRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDLD 123
           G F+ D L    +   ++   P + T FQLK R   GD P + YFRR SAA+H     LD
Sbjct: 63  GDFIKDQLAENQIGTDYISSTPDYWTAFQLKDRVSHGD-PSIFYFRRNSAAAHFEKRMLD 121

Query: 124 PA-LLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALMIR 182
                  +  H +GI PA+SD A +   +L+          +FDPNLRP LW S+  M  
Sbjct: 122 KIDFSGVKFAHLSGIFPAISDQALDAFKYLIQLLHEHNIRTTFDPNLRPQLWSSQEKMAG 181

Query: 183 EINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQG--AEAVVIKLGAHGAYYRTQL 240
            +N LA  A  +LPG  EG++L G DDP  IA FYL Q    + VV+K GA GAY +T+ 
Sbjct: 182 TLNELAKEAEIILPGDNEGKILVGSDDPKAIADFYLGQSDRTQTVVVKTGAKGAYVQTKA 241

Query: 241 -DAGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDME 299
            D+  V G  V QVVDTVGAGDGFA+GL++AL+E + + +AV RAN +G+ AVQ+ GD +
Sbjct: 242 GDSYTVPGFKVDQVVDTVGAGDGFALGLVTALMEGQSLRDAVIRANAVGAFAVQAPGDND 301

Query: 300 GLPLRHEL 307
           G P   +L
Sbjct: 302 GYPTPEKL 309


Lambda     K      H
   0.321    0.138    0.414 

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: 19
Number of successful extensions: 5
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: 320
Length of database: 318
Length adjustment: 28
Effective length of query: 292
Effective length of database: 290
Effective search space:    84680
Effective search space used:    84680
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 Sep 24 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