GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Pseudovibrio axinellae Ad2

Align BadH (characterized)
to candidate WP_068009499.1 PsAD2_RS18845 3-oxoacyl-[acyl-carrier-protein] reductase

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



>NCBI__GCF_001623255.1:WP_068009499.1
          Length = 245

 Score =  166 bits (419), Expect = 5e-46
 Identities = 91/253 (35%), Positives = 140/253 (55%), Gaps = 9/253 (3%)

Query: 1   MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAV 60
           M  L+ K+A++TG  GGIG A  R    +GA + +        E +A    D G      
Sbjct: 1   MFNLEGKSALVTGATGGIGEAIARSLHTQGATVTLSGTREAKLEALAA---DLGDRVHIK 57

Query: 61  RCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALH 120
             +++DR SVD  I      +G +DILVNNAG      F + +  EW++++ +NL+    
Sbjct: 58  AANLSDRDSVDELIPAAEEFMGGLDILVNNAGITRDNIFMRMKDEEWDQVLEVNLSATFR 117

Query: 121 MHHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITV 180
           +  A + GM++RRHGRI+ I S     G++G+  Y+A K G++  SK+LA+E A   ITV
Sbjct: 118 ICRAAIKGMMKRRHGRIIGITSIVGVTGNAGQVNYSAAKAGMIGMSKSLAQEVASRKITV 177

Query: 181 NVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFI 240
           N + PG   TA+  ++       EK  ++    +P GRLG  D++A A  +  SD+AG++
Sbjct: 178 NTIAPGFIATAMTDELN------EKQRDSILGNVPAGRLGTADEIASAAVYLASDEAGYV 231

Query: 241 TGQVLSVSGGLTM 253
           TGQ L V+GG+ M
Sbjct: 232 TGQTLHVNGGMAM 244


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: 172
Number of extensions: 6
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: 255
Length of database: 245
Length adjustment: 24
Effective length of query: 231
Effective length of database: 221
Effective search space:    51051
Effective search space used:    51051
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.

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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