GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Pseudomonas fluorescens FW300-N2C3

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate AO356_27985 AO356_27985 sorbitol dehydrogenase

Query= metacyc::MONOMER-16231
         (254 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27985
          Length = 257

 Score =  161 bits (407), Expect = 1e-44
 Identities = 99/261 (37%), Positives = 139/261 (53%), Gaps = 13/261 (4%)

Query: 1   MKLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIA 60
           MK LEGK+ LVTGA+ GIGRA A    + GA VAI    +D   +   A    LG  A A
Sbjct: 1   MKRLEGKSALVTGAARGIGRAFAQAYIEEGATVAI----ADIDLERANATAAELGDSAYA 56

Query: 61  VKGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAY 120
           VK DV D  +    +A  V   GK+D++++NA +      +D+     ER F +N+ G  
Sbjct: 57  VKMDVTDQASIDQAIAAVVAQAGKLDILINNAALFDLAPIVDITRQSYERLFSINVAGTL 116

Query: 121 FMVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGI 180
           F +QAAA+QM+RQGHGG I+ ++S +   G      Y  TKA V SL QS  + L KH I
Sbjct: 117 FTLQAAARQMIRQGHGGRIINMASQAGRRGEALVAVYCATKAAVISLTQSAGLDLIKHRI 176

Query: 181 RCNSVLPGTILTE---------INKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLA 231
             N++ PG +  E            ++L   EK+  +  + P GR+G  +DL G  +FLA
Sbjct: 177 NVNAIAPGVVDGEHWDGVDALFARHENLPQGEKKRQVGQQVPYGRMGTAQDLTGMAIFLA 236

Query: 232 SDMAAYVTGAALLVDGGMYVN 252
           S  + YV      VDGG +++
Sbjct: 237 SAESEYVVAQTYNVDGGNWMS 257


Lambda     K      H
   0.318    0.133    0.379 

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: 115
Number of extensions: 6
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: 254
Length of database: 257
Length adjustment: 24
Effective length of query: 230
Effective length of database: 233
Effective search space:    53590
Effective search space used:    53590
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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