GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Streptacidiphilus oryzae TH49

Align BadH (characterized)
to candidate WP_037570960.1 BS73_RS09090 3-oxoacyl-ACP reductase

Query= metacyc::MONOMER-893
         (255 letters)



>NCBI__GCF_000744815.1:WP_037570960.1
          Length = 274

 Score =  161 bits (408), Expect = 1e-44
 Identities = 103/255 (40%), Positives = 139/255 (54%), Gaps = 15/255 (5%)

Query: 3   RLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRC 62
           RL  ++AVITGGGGGIG AT RR A EGA++ V D++    EK   A  D  G    +R 
Sbjct: 23  RLVGRSAVITGGGGGIGLATARRLAAEGARVVVADVD----EKAGRAAADEVG-GLFMRT 77

Query: 63  DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKP----FTKTEPGEWERLIAINLTGA 118
           D+ D   V+A  A      G VD+  NNAG  I  P       T    W R+  +NLT  
Sbjct: 78  DVTDAEQVEALFAAAKEAYGSVDVAFNNAG--ISPPEDDSILTTGIDAWRRVQEVNLTSV 135

Query: 119 LHMHHAVLPGMVERRHGRIVNIASDAARVGSSGEAV-YAACKGGLVAFSKTLAREHARHG 177
                A LP M E+  G I+N AS  A +G++   + Y A KGG++A S+ L  + AR G
Sbjct: 136 YLCCKAALPYMREQGRGSIINTASFVAVMGAATSQISYTASKGGVLALSRELGVQFAREG 195

Query: 178 ITVNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDA 237
           I VN +CPGP DT LL ++   A +PE+        +P+GR  + D++A A+AF  SDDA
Sbjct: 196 IRVNALCPGPVDTPLLRELF--AKDPERARRRLVH-VPVGRFARADEIAAAVAFLASDDA 252

Query: 238 GFITGQVLSVSGGLT 252
            F+T     V GG++
Sbjct: 253 SFVTAAQFLVDGGIS 267


Lambda     K      H
   0.318    0.135    0.398 

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: 183
Number of extensions: 17
Number of successful extensions: 5
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: 255
Length of database: 274
Length adjustment: 25
Effective length of query: 230
Effective length of database: 249
Effective search space:    57270
Effective search space used:    57270
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