GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Lentibacillus jeotgali Grbi

Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate WP_010530530.1 ON01_RS08100 sugar kinase

Query= BRENDA::Q9WXS2
         (339 letters)



>NCBI__GCF_000224785.1:WP_010530530.1
          Length = 333

 Score =  209 bits (532), Expect = 8e-59
 Identities = 114/325 (35%), Positives = 177/325 (54%), Gaps = 6/325 (1%)

Query: 2   KVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLG 61
           K++T GE++LRL+P +H+R+     F   YGGAEANVA  L++ G D  F++  P N +G
Sbjct: 3   KILTMGELLLRLTPVNHQRLNIGGHFTANYGGAEANVAVSLSRFGHDVSFLSAFPPNDIG 62

Query: 62  DAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWE 121
           DAA  HL+  GV T  + R G R+GIYF E G S R  KV+YDR  S++ E   +  DW+
Sbjct: 63  DAALSHLQASGVDTSSVFRLGERLGIYFYEEGFSLRQGKVIYDRKASSVLELPDQYIDWD 122

Query: 122 KILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEAQKVM 181
           ++ D     H +GITP L K +       ++ A ++ V VS D NYR++LW  EEA++  
Sbjct: 123 QVYDEVDLLHVTGITPALSKGMKEFTLAGIQEAKKRNVQVSFDFNYRSKLWGVEEAKETF 182

Query: 182 IPFMEYVDVLIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTRKYNFKTVGITL 241
           +  + +VD+  A  +D   +LG   EG D    + ++E   +   E    Y  K +  T 
Sbjct: 183 LAILPHVDICFAGYKDFVYLLGF--EGPD----EFDKETLERFYREFAELYKIKYLASTR 236

Query: 242 RESISATVNYWSVMVFENGQPHFSNRYEIHIVDRVGAGDSFAGALIYGSLMGFDSQKKAE 301
           R   S + N  +  ++     + S+     I+DR+G GD+FA  +++  + G   ++  E
Sbjct: 237 RTVFSTSKNELTGYIYFEDYLYESDHVSFEILDRIGGGDAFASGVLHTIISGLAPEEVIE 296

Query: 302 FAAAASCLKHTIPGDFVVLSIEEIE 326
           F   +  LKH + GD+   S EE+E
Sbjct: 297 FGIGSGVLKHMVYGDYNQFSEEEVE 321


Lambda     K      H
   0.319    0.136    0.397 

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: 309
Number of extensions: 12
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: 339
Length of database: 333
Length adjustment: 28
Effective length of query: 311
Effective length of database: 305
Effective search space:    94855
Effective search space used:    94855
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 (21.8 bits)
S2: 49 (23.5 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