GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Lactobacillus silagei IWT126

Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_054655034.1 CES79_RS06025 ROK family glucokinase

Query= BRENDA::Q8R8N4
         (312 letters)



>NCBI__GCF_002217945.1:WP_054655034.1
          Length = 324

 Score =  196 bits (499), Expect = 5e-55
 Identities = 118/311 (37%), Positives = 165/311 (53%), Gaps = 1/311 (0%)

Query: 3   IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVKDV 62
           IG+DLGGT   +  V +DG I+   S PT      + I  +I     + +   G +    
Sbjct: 6   IGIDLGGTTTKIAFVSQDGDILQKWSIPTDISENGKHIVPNIITSLKKTMTDAGYTKDQF 65

Query: 63  KSMGIGVPGVADNEKGIVIRAVNLFW-TKVPLAKEIRKYIDLPIYMENDANVAALAEATF 121
             +G+G PG  D E G VI A NL W T   +  +I+  + L + +ENDANVAAL E   
Sbjct: 66  MGIGMGTPGAVDIENGTVIGAFNLNWKTTQHVRDQIQAGVGLQLVLENDANVAALGEFWK 125

Query: 122 GAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGCFE 181
           GAG   +  + +TLGTGVG G I  G++  G +  A EIGH+ +  NG  C CGK GC E
Sbjct: 126 GAGEKDQDVIFVTLGTGVGGGVIAGGQLLHGINGGAGEIGHITVQPNGYLCTCGKRGCLE 185

Query: 182 TYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEYVK 241
            Y+SAT ++   K  A        LK    + E +T+K V+  A   D  A +I ++   
Sbjct: 186 QYSSATGIVHVAKDMAAEFTGKSRLKELFDNHEEVTSKMVVYLADNGDILANRIVDKVSS 245

Query: 242 YLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKAELGN 301
           YL + + N  N+ +P  II+GGGV+ AG+ LL+P  +   EN          I+ A+LGN
Sbjct: 246 YLGLALANCANILNPANIIIGGGVSAAGNTLLQPTTRYFQENTFPAVRDSTRIKLAQLGN 305

Query: 302 DAGIIGAAILS 312
           DAG IGAA L+
Sbjct: 306 DAGAIGAASLA 316


Lambda     K      H
   0.318    0.140    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: 341
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: 312
Length of database: 324
Length adjustment: 27
Effective length of query: 285
Effective length of database: 297
Effective search space:    84645
Effective search space used:    84645
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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