GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Dinoroseobacter shibae DFL-12

Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate 3608646 Dshi_2039 Malate/L-lactate dehydrogenase (RefSeq)

Query= curated2:Q07251
         (349 letters)



>FitnessBrowser__Dino:3608646
          Length = 339

 Score =  131 bits (329), Expect = 3e-35
 Identities = 86/268 (32%), Positives = 123/268 (45%), Gaps = 14/268 (5%)

Query: 3   ISLTSARQLARDILAAQQVPADIADDVAEHLVESDRCGYISHGLSILPNYRTALDGHSVN 62
           +SL  AR L      A  VP   A   A+ LV ++  G + HG S L +Y        + 
Sbjct: 9   LSLPDARDLLFRAFTANGVPEGAARSTADALVAAEAEGQVGHGFSRLEDYVAQARSGKIV 68

Query: 63  PQGRAKCVLDQGTLMVFDGDGGFGQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGRMGH 122
                       T ++ D   GF     +  +   I   R+ G   + + RSHH G +  
Sbjct: 69  AGAEVTITRPAPTTLLVDAGHGFAYPALERAIDEGIAVARELGTAAIAVTRSHHCGALSI 128

Query: 123 YGEMAAAAGFVLLSFTNVINRAPVVAPFGGRVARLTTNPLCFAGPMPNGRPPLVVDIATS 182
           + E AA AG V +    V+N    +AP+GG+     TNP+ FA P   G  PLV+D++ S
Sbjct: 129 HVERAAKAGLVAMM---VVNAPAAIAPWGGKTPLFGTNPIAFATPRA-GSAPLVIDLSLS 184

Query: 183 AIAINKARVLAEKGEPAPEGSIIGADGNPTTDASTMFGEHPGALLPFGGHKGYALGVVAE 242
            +A  K     + G+P PEG  + A GNPTTDA    G   G ++P G  KG AL ++ E
Sbjct: 185 KVARGKVMNAKKAGKPIPEGWALDAAGNPTTDAEAALG---GTMVPIGEAKGTALALMVE 241

Query: 243 LLAGVLSG-------GGTIQPDNPRGGV 263
           +L+ V++G       G     D P  GV
Sbjct: 242 ILSAVMTGAALSTEAGSFFSADGPPPGV 269


Lambda     K      H
   0.319    0.136    0.409 

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: 319
Number of extensions: 15
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: 349
Length of database: 339
Length adjustment: 29
Effective length of query: 320
Effective length of database: 310
Effective search space:    99200
Effective search space used:    99200
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 (21.7 bits)
S2: 49 (23.5 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