GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Cupriavidus basilensis 4G11

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate RR42_RS37395 RR42_RS37395 glucokinase

Query= ecocyc::GLUCOKIN-MONOMER
         (321 letters)



>FitnessBrowser__Cup4G11:RR42_RS37395
          Length = 345

 Score =  220 bits (560), Expect = 4e-62
 Identities = 130/320 (40%), Positives = 180/320 (56%), Gaps = 8/320 (2%)

Query: 6   LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYL---EEHKVEVKDGCIA 62
           L+GDVGGTN R AL + A   I         D+PSLEA ++ YL          +   I 
Sbjct: 7   LLGDVGGTNVRFAL-ETAPQRIGPVTALKVADFPSLEAAVQHYLGGLPPGSARPRHAAIG 65

Query: 63  IACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGA 122
           +A P+TGD V +TNH WAFSI++M+++LG   L  INDFTA+++ +P L    L      
Sbjct: 66  LANPVTGDRVKLTNHAWAFSISQMQRSLGLDLLLAINDFTALALGLPHLGAHDLTLLRQG 125

Query: 123 EPVEGKPIAVYGAGTGLGVAHLVHVDKR-WVSLPGEGGHVDFAPNSEEEAIILEILRAEI 181
             V G P+A+ G GTGLGV+ LV       V+L GEGGH++  P +E+E       +   
Sbjct: 126 VAVTGAPLALVGPGTGLGVSGLVPARSGPAVALAGEGGHIELMPQTEDEWTAWRAAQQAF 185

Query: 182 GHVSAERVLSGPGLVNLYRAIVKADNRLP--ENLKPKDITERALADSCTDCRRALSLFCV 239
           G VSAER+LSG GL +L  A + A+   P    L+P ++TE A+      C RAL++FC 
Sbjct: 186 GRVSAERLLSGMGL-SLTHAALHAETGTPLARQLEPAEVTEGAIHRHDPLCERALAVFCG 244

Query: 240 IMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLI 299
           ++G    ++AL LG  GGV++ GGIVPRF+   + S F A F  KGR   Y+  +PVY+I
Sbjct: 245 LLGSVAADIALVLGARGGVYLGGGIVPRFVPALRNSAFNARFTAKGRLSAYLESLPVYVI 304

Query: 300 VHDNPGLLGSGAHLRQTLGH 319
               P L G    L + + H
Sbjct: 305 NAQYPALPGLAQALEEAITH 324


Lambda     K      H
   0.322    0.141    0.426 

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: 361
Number of extensions: 20
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: 321
Length of database: 345
Length adjustment: 28
Effective length of query: 293
Effective length of database: 317
Effective search space:    92881
Effective search space used:    92881
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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