GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Flavobacterium glycines Gm-149

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_066328574.1 BLR17_RS00650 SDR family oxidoreductase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_900100165.1:WP_066328574.1
          Length = 245

 Score =  100 bits (250), Expect = 2e-26
 Identities = 84/250 (33%), Positives = 125/250 (50%), Gaps = 23/250 (9%)

Query: 13  AVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQ 72
           A++TGG SGLG ATA++L   G    ++       EA  K++G   +    D+ + +++ 
Sbjct: 6   AIVTGGNSGLGFATAKKLCDNGIKTYIIGRTKDKTEAACKEIGPYAIPVIFDLNNLEEIP 65

Query: 73  TALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTH-TLEDFQRVLDVNLMGTFNVIRL 131
            A+     K   +D+ VN AGI       NLKK  T  T EDF  ++  NL+  F + R 
Sbjct: 66  -AMISELTKETSIDILVNNAGI-------NLKKEFTDVTDEDFLSIIHTNLLSVFAISRE 117

Query: 132 VAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGI 191
           V   M  N+       G IIN +S+A+  G     AYS+SKG I  MT  +A +LA  GI
Sbjct: 118 VVKNMKTNKG------GSIINISSMASQYGIPKVIAYSSSKGAIEAMTRAMAVELASFGI 171

Query: 192 RVMTIAPGLFGTPL----LTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQ--AIIENPF 245
           RV  IAPG   T +    L + PE+  N +  + P    LG+P + A      A  ++ +
Sbjct: 172 RVNCIAPGFIKTKMSSAALDNDPERK-NKVLGRTPM-GFLGEPDDIADAAYFFATADSKY 229

Query: 246 LNGEVIRLDG 255
           + G V+ +DG
Sbjct: 230 VTGTVLAVDG 239


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: 126
Number of extensions: 4
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: 245
Length adjustment: 24
Effective length of query: 237
Effective length of database: 221
Effective search space:    52377
Effective search space used:    52377
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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