GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Cronobacter universalis NCTC 9529

Align glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_038856588.1 AFK65_RS14270 oxidoreductase

Query= CharProtDB::CH_017124
         (365 letters)



>NCBI__GCF_001277175.1:WP_038856588.1
          Length = 362

 Score =  178 bits (451), Expect = 2e-49
 Identities = 127/371 (34%), Positives = 186/371 (50%), Gaps = 28/371 (7%)

Query: 3   RAIQSPGKYVQGADALQRLGDYLKP--LADSWLVIADKFVLGFAEDTIRQSLSKAGLAMD 60
           R +  P  Y     AL RLGD+  P  LA +  V  ++  +  A   +  ++   G    
Sbjct: 7   RVVPGPANYYSHPGALARLGDFYTPAQLARAVWVYGER-AMAAARPFLTDAIDAPGATR- 64

Query: 61  IVAFNGECSQGEVDRLCQLATQNGRSAIVGIGGGKTLDTAKAVAFFQKVPVAVAPTIAST 120
            + F G CS+ +V+ L   A  + R+ ++G+GGG  LDTAKA+A    +PV   PTIA+T
Sbjct: 65  -ILFRGHCSESDVNALAAQAGDD-RAVVIGVGGGALLDTAKALARRLGLPVVAIPTIAAT 122

Query: 121 DAPCSALSVLYTDEGEFDRYLMLPTNPALVVVDTAIVARAPARLLAAGIGDALATWFEAR 180
            A  + LSV Y D G+   + +      LV+V+  I+ RAPA  L AGIGD LA W+E  
Sbjct: 123 CAAWTPLSVWYNDAGQALHFEIFDDANHLVLVEPEIILRAPAEYLLAGIGDTLAKWYE-- 180

Query: 181 AASRSSAATMAGGPAT-----QTALNLARFCYDTLLEEGEKAMLAVQAQVVTPALERIVE 235
                 A  +A  PAT     +  LN A    D LLE+ E+A+ +     +T     +V+
Sbjct: 181 ------AVVLAPAPATLPLTVRLGLNAALAIRDVLLEQSEEALASQHRGALTQDFRDVVD 234

Query: 236 A----NTYLSGVGFESGGVAAAHAVHNGLTAVAETHHFYHGEKVAFGVLVQLALENASNA 291
           A       + G+G     VAAAHAVHNGLT + +T  + HG KVA+G+LVQ AL      
Sbjct: 235 AIIAGGGMVGGLGERYTRVAAAHAVHNGLTVLPQTEKYLHGTKVAYGILVQSALLGQDEV 294

Query: 292 EMQEVMSLCHAVGLPITLAQLDITEDIPTKMRAVAELACAPGETIHNMPGGVTVEQVYGA 351
            + +++       LP TLA+LD+      ++  V      P E+IH +P  ++      A
Sbjct: 295 -LAQLIDAWRRFRLPTTLAELDVDIHNAAELDRVIAHTLRPVESIHALPVALSP----AA 349

Query: 352 LLVADQLGQHF 362
           L  A +  +HF
Sbjct: 350 LRAAFEKVEHF 360


Lambda     K      H
   0.319    0.133    0.380 

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: 370
Number of extensions: 16
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: 365
Length of database: 362
Length adjustment: 29
Effective length of query: 336
Effective length of database: 333
Effective search space:   111888
Effective search space used:   111888
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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