GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Microvirga lotononidis WSM3557

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_009763228.1 MICLODRAFT_RS17985 ROK family transcriptional regulator

Query= BRENDA::Q8RDE9
         (315 letters)



>NCBI__GCF_000262405.1:WP_009763228.1
          Length = 417

 Score =  140 bits (353), Expect = 5e-38
 Identities = 98/311 (31%), Positives = 145/311 (46%), Gaps = 17/311 (5%)

Query: 7   GVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLEMSNLK 66
           G+++    IST +VD  G +     IP + +  P+ V+  I+  I          +  L 
Sbjct: 95  GIEIAADHISTLLVDIGGRVRAQRSIP-LPQNDPETVLPVIKAEIEAAQAQLEPPVPQLL 153

Query: 67  GIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAIGEHLFG 126
           G+G+  PGP N +    + P  L  W +   V  +   LG  V LENDA AAA+GE L G
Sbjct: 154 GVGVVMPGPFNVEGMTSVGPTTLSGWFDFDAVARIGDMLGAPVTLENDATAAAVGERLHG 213

Query: 127 SGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCNCGNYGCFEA 186
             R + NF  I    G+G G++I+G+ Y G N NA EIGH  +   G  C+CG +GC EA
Sbjct: 214 VARNLKNFCLIYFGQGLGLGIMIDGRPYRGANGNAGEIGHVRVAKGGRLCSCGQHGCLEA 273

Query: 187 YASGTAIA-RFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKELVEKEAFYL 245
           YAS  ++A + A  GI      +++ L  E     +H    A          +E+ A YL
Sbjct: 274 YASFHSLAQKLAAAGIHGIDYAELERLHRE-----KHPVVLA---------WIEEAAGYL 319

Query: 246 GVGIANIMAFYNPRKIAIGGGV-SAQWDMLYEKMMETVRKKALKPNAEVCEVVKAQLGEN 304
              +A +   ++P  I +GG +     + L E M       A + N     ++  + G  
Sbjct: 320 APQVAMLENLFDPEAIVLGGVLPPGLLEDLVEAMQPLPLSVARRRNRSEARLIHGRTGGL 379

Query: 305 IGVLGAAALLL 315
              LGAAAL L
Sbjct: 380 TAALGAAALPL 390


Lambda     K      H
   0.316    0.138    0.398 

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: 311
Number of extensions: 17
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: 315
Length of database: 417
Length adjustment: 29
Effective length of query: 286
Effective length of database: 388
Effective search space:   110968
Effective search space used:   110968
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 (21.6 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