GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Dinoroseobacter shibae DFL-12

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate 3608790 Dshi_2182 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)

Query= metacyc::MONOMER-16230
         (256 letters)



>FitnessBrowser__Dino:3608790
          Length = 245

 Score =  140 bits (352), Expect = 3e-38
 Identities = 96/249 (38%), Positives = 138/249 (55%), Gaps = 10/249 (4%)

Query: 3   LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62
           L  KT +VTGAS GIG A A     QGA V  G SG+      AL+     A  G  A  
Sbjct: 4   LTGKTALVTGASGGIGGAIATALHAQGATV--GLSGTRVDPLEALA-----AELGERAHV 56

Query: 63  VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122
           +  + +D D+ E L   AV A GSVD+LVNNAGI   + F+ M  E +   +  NL    
Sbjct: 57  LPCNLSDADAVEALPKQAVAAMGSVDILVNNAGITRDNLFMRMSDEEWASVLDVNLTSTM 116

Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182
              +   R M +  R G I+ +SS+    G   Q +Y  +KAG++ + +S A  +   GI
Sbjct: 117 RLCRGVLRGMMK-ARWGRIVNISSVVGATGNPGQGNYAASKAGMVGMSKSLAYEVASRGI 175

Query: 183 RCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTG 242
             NAV PG I+T +  + L+D ++++++  +VP GR+GEP ++A  +V+LAS  A YVTG
Sbjct: 176 TVNAVAPGFISTAMT-DKLTD-DQKDKLLVQVPSGRMGEPGEIAAAVVYLASPEAGYVTG 233

Query: 243 ASLLVDGGL 251
           + L V+GGL
Sbjct: 234 SVLHVNGGL 242


Lambda     K      H
   0.319    0.136    0.383 

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: 159
Number of extensions: 6
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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