GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Phaeobacter inhibens BS107

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate GFF2759 PGA1_c28020 fructokinase Frk

Query= reanno::Dino:3609413
         (308 letters)



>FitnessBrowser__Phaeo:GFF2759
          Length = 323

 Score =  292 bits (748), Expect = 6e-84
 Identities = 165/322 (51%), Positives = 199/322 (61%), Gaps = 17/322 (5%)

Query: 1   MILCAGEALIDMLPR----ALP-----DGTAGFAPVAGGAVFNTAVALGRLGADVGLVTG 51
           MILC GEALIDM+P     A+P     D   GF P  GGAVFNTA+ALGRLG   GL TG
Sbjct: 1   MILCCGEALIDMIPAPVAGAVPVVDGADAQTGFVPHCGGAVFNTAIALGRLGQTTGLFTG 60

Query: 52  LSRDLFGEVLMTALAAADVDSDMAVLSDRPTTLAFVTLTDGHAQYAFYDENTAGRMLAPA 111
           LSRDLFG+ L  AL A+ VD   A  SD+P+TLAFV L DGHA+Y F+DEN+AG  L P 
Sbjct: 61  LSRDLFGQQLAAALVASHVDHGFAERSDQPSTLAFVHLRDGHAEYHFFDENSAGASLRPD 120

Query: 112 DMPDPGPEVGTLFFGGISLAVEPCAAAYEALCLKAAAGRVVMLDPNIRPGFIKDETTFRA 171
            +P+   +V  LFFGGISL     A  Y AL  +    R++M+DPN+R GF KDE  +R+
Sbjct: 121 RLPELSADVDALFFGGISLCNGAAAETYAALAARERGRRIIMIDPNVRAGFAKDEAAYRS 180

Query: 172 RIDRMLAVTDIVKVSDEDLAWLMGPGD------LAESAAALRARGPAVVCVTRGGAGVEA 225
           R+  M+A   IVKVSDEDL W+  PGD      + +        GP +V +T G  G + 
Sbjct: 181 RLAAMVARAGIVKVSDEDLHWIY-PGDAPIEEKIRQILTGEAGMGPGLVILTLGSKGAKG 239

Query: 226 HTATGIT-HVAAEAVEVVDTVGAGDTFNAGFLAGLAEAGALDKDRLRALDAPVLTSALRL 284
              +G T  V A+   V DTVGAGDTFNAGF+A   EAG L       +D   L   L  
Sbjct: 240 FLRSGPTVEVPAQVAVVADTVGAGDTFNAGFMAAATEAGVLADAASGEMDPEQLRVCLGY 299

Query: 285 GAQAAAITVSRAGANPPWRDEL 306
           GA+AAA+TVSR GANPPWRDEL
Sbjct: 300 GARAAAVTVSRPGANPPWRDEL 321


Lambda     K      H
   0.320    0.136    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: 293
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: 308
Length of database: 323
Length adjustment: 27
Effective length of query: 281
Effective length of database: 296
Effective search space:    83176
Effective search space used:    83176
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 17 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