GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Marivita geojedonensis DPG-138

Align Glucokinase; EC 2.7.1.2 (characterized, see rationale)
to candidate WP_085638909.1 MGEO_RS13935 glucokinase

Query= uniprot:A8LLL9
         (323 letters)



>NCBI__GCF_002115805.1:WP_085638909.1
          Length = 322

 Score =  308 bits (788), Expect = 2e-88
 Identities = 162/321 (50%), Positives = 216/321 (67%), Gaps = 4/321 (1%)

Query: 1   MTSLRDAPALVADIGGTNTRVALADGPVLRAGSVEKYRNADYSSLDSVLRSYL-EKMEVA 59
           MT      ALVAD+GGTNTRVAL DG  +R  +++++RNA++  L SVLR+YL ++  V 
Sbjct: 1   MTETTPVTALVADLGGTNTRVALTDGGAVRTDTIKRFRNAEHPDLLSVLRAYLADQTVVP 60

Query: 60  GCSGACVALAGPVRNGIGHLTNLDWRMDEDLLSEATGAPVVALLNDLQAQGFALGHLEAA 119
            C  ACVA+AGPVR+G+G LTNL W +D D +++ATGA  VA+LNDLQAQG AL  L+  
Sbjct: 61  DC--ACVAMAGPVRDGVGELTNLSWTVDRDSVADATGAKTVAVLNDLQAQGHALDLLKPE 118

Query: 120 CLRPVISRPPPAAQETRLMIGLGTGFNAASVLYTPAGRIVTPSEAGHANLPVRTEQELRL 179
            L+ ++       +  RL+IG+GTG NAA+V       +V PSEAGH +LP +   ELRL
Sbjct: 119 VLQTILPGQKTGPKAARLVIGIGTGMNAAAVYRLGDRTLVPPSEAGHVSLPAQNADELRL 178

Query: 180 CRFVETAHGFPAVEDVLSGRGLERVYNFLSPTPDQPQRLSAAEVMAAA-AREERQALDAL 238
             ++   HG P +ED+LSGRG ERVY +L         L A+ +M A      + A +A 
Sbjct: 179 LDWIAKKHGTPGLEDILSGRGFERVYEWLCSEAGVDAPLDASGIMQAVNDGSSKIAEEAA 238

Query: 239 ELFIGLLGTVAGNLSLIHLPFGGVYLCGGVARHIGPYLGSMGFAEAFANKGRFADFMRDF 298
            +F+ ++G  AGNL+L+HLPFGG+YL GGVARH  P+L  +GF EAF +KGRF++FM  F
Sbjct: 239 RMFVRMMGRAAGNLALVHLPFGGIYLIGGVARHFAPHLERLGFREAFHDKGRFSEFMEQF 298

Query: 299 PVWLVEDDFAALTGCASFLDE 319
           PV LVEDD+AALTG A+ L E
Sbjct: 299 PVHLVEDDYAALTGSAAHLME 319


Lambda     K      H
   0.321    0.137    0.412 

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: 339
Number of extensions: 16
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: 323
Length of database: 322
Length adjustment: 28
Effective length of query: 295
Effective length of database: 294
Effective search space:    86730
Effective search space used:    86730
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