GapMind for catabolism of small carbon sources

 

Aligments for a candidate for scrK in Dinoroseobacter shibae DFL-12

Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate 3608582 Dshi_1976 PfkB domain protein (RefSeq)

Query= SwissProt::A2WXV8
         (323 letters)



>lcl|FitnessBrowser__Dino:3608582 Dshi_1976 PfkB domain protein
           (RefSeq)
          Length = 305

 Score = 94.7 bits (234), Expect = 2e-24
 Identities = 94/297 (31%), Positives = 143/297 (48%), Gaps = 33/297 (11%)

Query: 32  AFVKAPGGAPANVAIAVARLGGGAAFVGKLGDDEFGRMLAAILRDNGVDDGGVVFDAGAR 91
           +F   PGG  +N AIA A+ GG A F+ +LG+D F  M AAI  + GV       D  + 
Sbjct: 33  SFALNPGGKGSNQAIAAAKSGGDARFLTRLGEDAFADMAAAIWAEAGV-RATAPRDPASY 91

Query: 92  TALAFVTL-RADGEREFMFYRNPSADMLLTHAELN--VELIKRAAVFHYGSISLIAEPCR 148
           T  A++ +  A G+   +    P A  LL  A+L+   E+I  A VF    ++ + +P  
Sbjct: 92  TGAAYIYVDPATGDNAIIV--APGAAALLGPADLDAQAEMIGGAGVF----LTQLEQPMP 145

Query: 149 SAHLRAMEIAKEAGALLSYDPNLREALWPSREEARTKILSIWDHADIVKVSEVELEFLTG 208
           +A  R +EIA+ AG     +P     L    ++A   +       DIV  +E E E LTG
Sbjct: 146 AAR-RGLEIARAAGVTTILNPAPAAPL----DDALLAL------CDIVTPNETEAEALTG 194

Query: 209 IDSVEDDVVMK----LWRPTMKLLLVTLGDQGCKYYARDFRGAVPSYKV-QQVDTTGAGD 263
                 D  ++    L       ++VTLG QG  Y +       P++     V+TTGAGD
Sbjct: 195 HPVTGPDDAVRAADALLARGPGAVIVTLGAQGVLYRSATQTIHQPAFTPGPVVETTGAGD 254

Query: 264 AFVGALLRRIVQDPSSLQDQKKLEEAIKFANACGAITATKKGAIPSLPTEVEVLKLM 320
           AF GAL        ++L + +    A++F  A  +I+ T+ GA PS+P+  E+  L+
Sbjct: 255 AFNGAL-------ATALAEGQDTASALRFGCATASISVTRPGAGPSMPSRAEIDALL 304


Lambda     K      H
   0.320    0.136    0.389 

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: 237
Number of extensions: 8
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: 323
Length of database: 305
Length adjustment: 27
Effective length of query: 296
Effective length of database: 278
Effective search space:    82288
Effective search space used:    82288
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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