GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lldE in Pseudomonas fluorescens FW300-N2E3

Align Uncharacterized protein (characterized, see rationale)
to candidate AO353_05705 AO353_05705 oxidoreductase

Query= uniprot:B2TBW0
         (256 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05705
          Length = 274

 Score =  145 bits (366), Expect = 9e-40
 Identities = 96/246 (39%), Positives = 128/246 (52%), Gaps = 16/246 (6%)

Query: 11  KVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTERV 70
           +V LF  C +D FYPE G+  + LLER GI+V+YPQ Q+CCGQP   SG   +A    R 
Sbjct: 32  RVYLFGTCVVDLFYPEAGMDAIHLLEREGIRVEYPQGQSCCGQPAYTSGYTEQARTVARS 91

Query: 71  FARNFAGYDYIVGPSASCIHHVREHLTAL--EQTDEVKKVRANA---YELVEFLHDVVGA 125
               FAG   +V PS SC   +REH   L  ++ D +K+V+A A   YEL EFL  V   
Sbjct: 92  QLALFAGDYPVVVPSGSCAGMLREHYADLFKDEPDTLKQVQALAARTYELAEFLLFVCKV 151

Query: 126 REFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDE 185
            +   +  P +V LH SCSA R +     + + G      R LL  +  ++ V      E
Sbjct: 152 -QLKDSGKPVKVALHTSCSARREMN----THLHG------RELLSQLSNVKRVDHDHESE 200

Query: 186 CCGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFI 245
           CCGFGGTFSV    +S  M  DK +    +GA  ++S D  CLM+  G  E+     R  
Sbjct: 201 CCGFGGTFSVRMPDISGAMVADKTKALKESGAHTVLSADCGCLMNINGSLEKQNEALRGQ 260

Query: 246 HIAQVL 251
           H+A  L
Sbjct: 261 HLASFL 266


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: 249
Number of extensions: 14
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: 274
Length adjustment: 25
Effective length of query: 231
Effective length of database: 249
Effective search space:    57519
Effective search space used:    57519
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: 47 (22.7 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