GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Herbaspirillum seropedicae SmR1

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate HSERO_RS02925 HSERO_RS02925 3-oxoacyl-ACP reductase

Query= SwissProt::Q1NEI6
         (249 letters)



>FitnessBrowser__HerbieS:HSERO_RS02925
          Length = 244

 Score =  209 bits (531), Expect = 5e-59
 Identities = 111/241 (46%), Positives = 155/241 (64%), Gaps = 8/241 (3%)

Query: 10  GRC-AIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVVALDVSDHA 68
           G C A+VTGG  G+G  ++AR+ A G  V +WD + DA +  + +       ++D++D  
Sbjct: 11  GDCVAVVTGGHGGIGAAISARLAAGGAQVVVWDQHHDAASPYRQQ-------SIDITDAP 63

Query: 69  AVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREVVP 128
           AV  AA++  A  G++D LI +AG  G TVP+ E+ V  + R++ +NL G+F+  R V P
Sbjct: 64  AVMQAAQELLADTGRIDFLINNAGYAGPTVPLDEYDVGEWHRIVQVNLLGVFHACRSVTP 123

Query: 129 FMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTPAT 188
            M     GRIVN+AS+AGKEG PNASAYSA+KAGV+  TKSLGKELA  GV+ NA+ PA 
Sbjct: 124 AMRAARRGRIVNIASLAGKEGTPNASAYSAAKAGVLALTKSLGKELAESGVLVNAIAPAA 183

Query: 189 FESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGGRTT 248
            ++ +L Q+  + V  M +K PM RLG V+E A M  ++ S  CSF T + FD SGGR T
Sbjct: 184 VKTALLGQMSPAHVQTMIAKSPMHRLGSVDEVADMCAWLCSGSCSFNTGAVFDLSGGRAT 243

Query: 249 F 249
           +
Sbjct: 244 Y 244


Lambda     K      H
   0.318    0.132    0.381 

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: 174
Number of extensions: 10
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: 249
Length of database: 244
Length adjustment: 24
Effective length of query: 225
Effective length of database: 220
Effective search space:    49500
Effective search space used:    49500
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: 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