GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pontibacter ramchanderi LP43

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate WP_101443621.1 BD749_RS04795 glucose 1-dehydrogenase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_002846395.1:WP_101443621.1
          Length = 247

 Score =  129 bits (323), Expect = 8e-35
 Identities = 90/256 (35%), Positives = 130/256 (50%), Gaps = 17/256 (6%)

Query: 10  GLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEA---QAKKLGNNCVFAPADVT 66
           G VA++TGG+SG+G + A     +GA  V+ D+    G     + ++LG+  +F  ADV+
Sbjct: 4   GKVALVTGGSSGIGRSAALLYAREGAKVVVSDIHEESGMQVVREIEQLGSQAIFVAADVS 63

Query: 67  SEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTF 126
              D +  +  A  KFGR+DVA N AGI   S T         ++E + +V+ +NL   F
Sbjct: 64  KPADCERMVQQAVEKFGRLDVAFNNAGIGGESNTIG-----DMSIEGWDKVISINLNSVF 118

Query: 127 NVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDL 186
             +     +M Q    QGG  G I+N +S+    G    AAY A+K G+VG+T     + 
Sbjct: 119 YCMHFQIRQMLQ----QGG--GAIVNNSSILGQVGFANSAAYVAAKHGVVGLTKNGGLEY 172

Query: 187 APIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIEN--P 244
           A  GIR+  I P    TPLL+ + E+   FL S+ P   RLG P E A LV  +  N   
Sbjct: 173 ASKGIRINAIGPAFIKTPLLSGMGEETLQFLTSKHPI-GRLGAPEEIAELVIWLSSNKAS 231

Query: 245 FLNGEVIRLDGAIRMQ 260
           F++G     DGA   Q
Sbjct: 232 FVSGAYYAADGAYLSQ 247


Lambda     K      H
   0.318    0.135    0.385 

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: 153
Number of extensions: 9
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: 261
Length of database: 247
Length adjustment: 24
Effective length of query: 237
Effective length of database: 223
Effective search space:    52851
Effective search space used:    52851
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 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