GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lldE in Pedobacter sp. GW460-11-11-14-LB5

Align Uncharacterized protein (characterized, see rationale)
to candidate CA265_RS07800 CA265_RS07800 Fe-S oxidoreductase

Query= uniprot:B2TBW0
         (256 letters)



>FitnessBrowser__Pedo557:CA265_RS07800
          Length = 245

 Score =  172 bits (437), Expect = 4e-48
 Identities = 98/246 (39%), Positives = 136/246 (55%), Gaps = 15/246 (6%)

Query: 10  MKVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTER 69
           MKV LF+PCF+D  YPE    TL LLE+ G  V Y  +QTCCGQP  N+G   EA     
Sbjct: 1   MKVELFVPCFVDQLYPETAFNTLRLLEKSGCDVTYNSKQTCCGQPAYNAGYWDEAKEVGT 60

Query: 70  VFARNFAGYDYIVGPSASCIHHVR----EHLTALEQTDEVKKVRANAYELVEFLHDVVGA 125
            F  +F    Y+V PSASC+  V+    +  T     ++ + +++N +EL +FL + V  
Sbjct: 61  KFLNDFTENTYVVAPSASCVGMVKGGFNDLFTNTIVHNKCRSLQSNIWELSDFLIN-VAK 119

Query: 126 REFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDE 185
           R++  AE   +   H+SCSALR  K             +PR LL  V G+E ++    D 
Sbjct: 120 RDYFGAELEGKAVYHDSCSALRECKIK----------DEPRQLLSKVHGLEMIEMEDTDM 169

Query: 186 CCGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFI 245
           CCGFGGTF+V  + +S  M + KV   L   A+YI+S D+SCL+H QG  E+     + +
Sbjct: 170 CCGFGGTFAVKFDAISSAMAEQKVNHALAQQADYIISTDLSCLLHLQGYIEKNNLPIKTM 229

Query: 246 HIAQVL 251
           HIA VL
Sbjct: 230 HIADVL 235


Lambda     K      H
   0.323    0.137    0.422 

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: 173
Number of extensions: 7
Number of successful extensions: 4
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: 256
Length of database: 245
Length adjustment: 24
Effective length of query: 232
Effective length of database: 221
Effective search space:    51272
Effective search space used:    51272
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 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