GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Sporolactobacillus vineae SL153

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_010631476.1 RH97_RS06160 ROK family protein

Query= BRENDA::B1VZT1
         (313 letters)



>NCBI__GCF_000246965.1:WP_010631476.1
          Length = 297

 Score = 83.2 bits (204), Expect = 7e-21
 Identities = 85/322 (26%), Positives = 134/322 (41%), Gaps = 54/322 (16%)

Query: 6   GVDIGGTKIAAGVVDEEGRILSTFKVATPPTAEGIVDAICAAVAGASEGHDVEAVGIGAA 65
           G++ GGTK    V DE G +L+  ++AT        D     V    +   ++++GI + 
Sbjct: 5   GIEAGGTKFVCAVGDESGNVLAKERIATKDP-----DYTMDRVIHFFKNFQIDSLGIASF 59

Query: 66  GYVD-----DKRATVLFAPNIDWRHEPLKDKVEQRVGLPVVVENDANAAAWGEYRFGAGQ 120
           G +D         ++   P   W + P    ++  + LPV    D N AA GE   GA +
Sbjct: 60  GPIDLDPESAAYGSITSTPKPGWANYPFVGTMKDALHLPVGFTTDVNGAALGELYHGAAK 119

Query: 121 GHDDVICITLGTGLGGGIIIGNKLRRGRFGVAAEFGHI---RVVPDGLLCGCG-SQGCWE 176
           G D  + +T+GTG+G G++  N+L +G      E GHI   R   D     C   + C E
Sbjct: 120 GLDGCLYLTVGTGIGAGLVNRNQLFQGL--SHPEMGHILVRRSPKDHFEGICPYHKDCLE 177

Query: 177 QYASGRALVRYAKQRANATPENAAVLLGLGDGSVDGIEGKHISEAARQGDPVAVDSFREL 236
             ASG AL    K R                       GK  SE      P   ++++  
Sbjct: 178 GVASGPAL----KAR----------------------WGKSASEL-----PADHEAWQME 206

Query: 237 ARWAGAGLADLASLFDPSAFIVGGGVSDEGELVLDPIRKSFRRWLIGGEWRPHAQ----- 291
           A +    L     +  P   I+GGGV  + +L    IR++ +  L G    P  +     
Sbjct: 207 ADYLAQALMQYILIVSPKRIIIGGGVMKQKQL-FPMIRRNVQELLAGYIDFPEVRGGIDS 265

Query: 292 -VLAAQLGGKAGLVGAADLARQ 312
            ++  +LG  +G+ GA  LA++
Sbjct: 266 YIVPPELGDNSGITGALILAKR 287


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: 213
Number of extensions: 14
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 313
Length of database: 297
Length adjustment: 27
Effective length of query: 286
Effective length of database: 270
Effective search space:    77220
Effective search space used:    77220
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: 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