GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguK in Salinicoccus carnicancri Crm

Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate WP_017549879.1 C792_RS0112925 sugar kinase

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



>NCBI__GCF_000330705.1:WP_017549879.1
          Length = 315

 Score =  154 bits (388), Expect = 4e-42
 Identities = 104/302 (34%), Positives = 152/302 (50%), Gaps = 9/302 (2%)

Query: 4   IDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSL 63
           ++++  GE+M   V E  G +     F   +AGA+ N  IGL+RLG   +W+S +G D L
Sbjct: 1   MEVIGIGESMVALVNEPKGYIRHADSFKPYVAGAEMNTLIGLSRLGHGTSWVSALGEDEL 60

Query: 64  GRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDLD 123
           G  +L  +RAE +D   V         F  +   DG  D  V Y+R  SAAS++ I D+D
Sbjct: 61  GELILHKVRAENVDASHVTHKDKRTGVFFKQILPDGSVD--VTYYREDSAASNMDIRDID 118

Query: 124 -PALLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVS--FDPNLRPALWPSEALM 180
             A+ RA+ L+ TGI  +LS SA+E+   L    R AG  V+  FDPN+R  +W ++   
Sbjct: 119 MDAIRRAKVLYLTGITLSLSSSAKEM---LFEAVRIAGDDVTVVFDPNIRLKMWSAKEAR 175

Query: 181 IREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQL 240
              I         ++ G  E  +L G   P +    + + G   VV+KLG  GA Y    
Sbjct: 176 -ETILEFLPHVDCLIAGRDEVDILMGAMRPEEALKSFRELGCSKVVLKLGKEGAVYDFDG 234

Query: 241 DAGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEG 300
             G V+     + +D VGAGD FA G+IS LL       +V++A ++G    Q  GD +G
Sbjct: 235 IGGSVKNPKQFEEIDPVGAGDAFAAGIISGLLNGEDPEASVEKACFLGGYITQFVGDYQG 294

Query: 301 LP 302
            P
Sbjct: 295 FP 296


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: 279
Number of extensions: 18
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: 315
Length adjustment: 27
Effective length of query: 293
Effective length of database: 288
Effective search space:    84384
Effective search space used:    84384
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