GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Salinicoccus carnicancri Crm

Align Fructokinase; EC 2.7.1.4 (uncharacterized)
to candidate WP_017548855.1 C792_RS0107525 ROK family glucokinase

Query= curated2:Q03417
         (301 letters)



>NCBI__GCF_000330705.1:WP_017548855.1
          Length = 319

 Score = 73.9 bits (180), Expect = 4e-18
 Identities = 88/315 (27%), Positives = 124/315 (39%), Gaps = 45/315 (14%)

Query: 14  GGTKFMLALIDSDRKMLAVERVPTTTPEE---TLGKSVEFFK---KALPQYADSFASFGI 67
           GGT   L + D +  ++    +PT   EE    L   ++ F+   + L    +     G+
Sbjct: 10  GGTSCKLGVFDEELNLIEKWEIPTDISEEGSHILADVLDSFRSKEEILGFKVEECLGTGL 69

Query: 68  ASFGPLCLDRKSPKWGYITNTPKPFWPNTDVVTPFKEAFGCPVEIDTDVNGAALAENFWG 127
              GP+  + K    G I    K       + T F E  G    +D D N AAL E   G
Sbjct: 70  GMPGPVDFE-KGILNGCINLNIKG---KRSIATIFSELSGSAAIVDNDANVAALGEQSKG 125

Query: 128 ASKGTHTSVYVTVGTGFGGGVLIDGKPIHGLAHPEMGHGIPIRHPDDRDFEG---CCPYH 184
           A  G    V +T+GTG GGGV+ +G+ IHG      G G  I H    DF+G   C    
Sbjct: 126 AGHGHSEVVMITLGTGVGGGVISEGRLIHGTG----GSGGEIGHITV-DFDGRFQCNCGK 180

Query: 185 GGCYEGLASGTAIRKRWGKALNEMEPAEF-------------------------EKAREI 219
            GC E +AS T +    G   ++ E +                           E   E 
Sbjct: 181 KGCLETVASATGMVNLAGYHSDDHENSVLIAAIKEGTLTSKAIVDAAMTGDPLAEFVVEE 240

Query: 220 IAFYLAHFNVTLQAFISPERIVFGGGVMHVDGMLASVRRQTAEIANSYFEGADFEKIIVL 279
            A YLA    ++    +P   VFGGGV      L    ++  +  +  F  A  +  IV+
Sbjct: 241 AARYLAVAMSSISVITNPGYFVFGGGVSRAGRYLTDKIKKYYD--SLIFPPAADDVEIVM 298

Query: 280 PGLGDQAGMMGAFAL 294
             LG+ AGM GA  L
Sbjct: 299 AELGNDAGMYGAARL 313


Lambda     K      H
   0.320    0.139    0.435 

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: 227
Number of extensions: 14
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 301
Length of database: 319
Length adjustment: 27
Effective length of query: 274
Effective length of database: 292
Effective search space:    80008
Effective search space used:    80008
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 (21.8 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