GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguK in Halococcus hamelinensis 100A6

Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate WP_049904537.1 C447_RS14190 sugar kinase

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



>NCBI__GCF_000336675.1:WP_049904537.1
          Length = 318

 Score =  229 bits (583), Expect = 9e-65
 Identities = 133/303 (43%), Positives = 174/303 (57%), Gaps = 2/303 (0%)

Query: 6   ILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSLGR 65
           +++ GETM +      G +     F K +AGA++NVAIGLARLG  V W S++G D  G 
Sbjct: 5   VVTLGETMVLVYPSTTGPMKHAHEFEKSLAGAETNVAIGLARLGHDVGWYSKLGTDPHGE 64

Query: 66  FVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDLD-P 124
           ++   +R EG+D   V      PTG   K R + G+ P V Y+R GSAAS ++  DL   
Sbjct: 65  YLEFFVRGEGVDTTTVEFTDEAPTGIMFKERREFGE-PAVHYYRHGSAASLMSPDDLPVD 123

Query: 125 ALLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALMIREI 184
            L  A +LH TGI PALS+S R+ +         AG +VSFDPN+R  LW S+  M   +
Sbjct: 124 YLTNAEYLHLTGITPALSESCRDATLLAAERATEAGMTVSFDPNVRRKLWESDERMRETM 183

Query: 185 NRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQLDAGF 244
             L +L+  VLPG+ EG  L G DDP  IAA  LD GA   V+KLGA GA          
Sbjct: 184 LDLVSLSDIVLPGIEEGAALFGTDDPEAIAAACLDHGAGTAVVKLGAAGAVVADGSTTER 243

Query: 245 VEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEGLPLR 304
           V G  V +VVD VGAGDGFA G +++ +E +G +EA + AN +G+ A    GD EGLP R
Sbjct: 244 VSGYDVERVVDPVGAGDGFAAGFLASRIEGQGPVEATETANAVGAFATTVAGDTEGLPTR 303

Query: 305 HEL 307
            EL
Sbjct: 304 KEL 306


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: 308
Number of extensions: 15
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: 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