GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_1862 Echvi_1862 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= BRENDA::Q99714
         (261 letters)



>FitnessBrowser__Cola:Echvi_1862
          Length = 246

 Score =  111 bits (277), Expect = 2e-29
 Identities = 79/251 (31%), Positives = 128/251 (50%), Gaps = 22/251 (8%)

Query: 12  VAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDV 71
           +A++TGGASGLGLATA++      + +++    S      ++LG NC +   D+    ++
Sbjct: 5   IALVTGGASGLGLATAKKFCDHDITTIIIGRNESKLAKAQEELGPNCHYYAFDLNDLPNI 64

Query: 72  QTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTH-TLEDFQRVLDVNLMGTFNVIR 130
              +     + G++D+ VN AGI       N+KK     T E+FQ+++  N+   F++ R
Sbjct: 65  PDLINTITTEHGKIDILVNNAGI-------NMKKPFIEVTDEEFQQIITTNVFAVFSLSR 117

Query: 131 LVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIG 190
            +A  M         + G I+N +S+A+  G     AY+ASK  I GMT  +A +L+P+G
Sbjct: 118 EIAKTMASQ------KHGAIVNISSMASQYGIPKVIAYTASKSAIEGMTKAMAVELSPLG 171

Query: 191 IRVMTIAPGLFGTPL----LTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIEN--P 244
           IRV  +APG   T +    L   PE+    L S+ P    LG PA  A  V  +      
Sbjct: 172 IRVNCVAPGFIATEMSAKALNGDPERKQKVL-SRTPM-GALGTPANIADAVYYLASESAS 229

Query: 245 FLNGEVIRLDG 255
           ++ G ++ +DG
Sbjct: 230 YITGTILPVDG 240


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: 143
Number of extensions: 12
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: 246
Length adjustment: 24
Effective length of query: 237
Effective length of database: 222
Effective search space:    52614
Effective search space used:    52614
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