GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Phyllobacterium brassicacearum STM 196

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_106713292.1 CU102_RS22250 ROK family transcriptional regulator

Query= BRENDA::B1VZT1
         (313 letters)



>NCBI__GCF_003010955.1:WP_106713292.1
          Length = 404

 Score = 72.0 bits (175), Expect = 2e-17
 Identities = 62/181 (34%), Positives = 85/181 (46%), Gaps = 24/181 (13%)

Query: 83  WRHEPLKDKVEQRVGLPVVVENDANAAAWGEYRFGAGQGHDDVICITLGTGLGGGIIIGN 142
           W++ PL D++ +  GL V ++NDA AAA  E   GA  G D  ICI  G GLG G+I+  
Sbjct: 180 WQNFPLIDRIAEGTGLEVALQNDAAAAATAERLLGAAHGLDHAICIYFGYGLGTGLILNG 239

Query: 143 KLRRGRFGVAAEFGHI-RVVP-DGLLCGCGSQGCWEQYASGRALVRYAKQRANATPENAA 200
           +L  G    A E G I  +VP DGL          E YAS  AL +              
Sbjct: 240 ELYGGAHSNAGEIGMILALVPGDGL-----DVEPLEHYASMAALCK-------------- 280

Query: 201 VLLGLGDGSVDGIEGKHISEAARQGDPVAVDSFRELARWAGAGLADLASLFDPSAFIVGG 260
            LL L D S   + G+ +++A   G P   +    +A+     +  L S+FDP   I+ G
Sbjct: 281 -LLNL-DPSEPELFGQ-VTDALMHGGPKLDEWIGNVAQRLRRTVQALESIFDPQTIILCG 337

Query: 261 G 261
           G
Sbjct: 338 G 338


Lambda     K      H
   0.319    0.140    0.427 

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: 322
Number of extensions: 21
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: 313
Length of database: 404
Length adjustment: 29
Effective length of query: 284
Effective length of database: 375
Effective search space:   106500
Effective search space used:   106500
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 (21.7 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