GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Acidovorax sp. GW101-3H11

Align BadH (characterized)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2257
          Length = 267

 Score =  135 bits (340), Expect = 9e-37
 Identities = 83/249 (33%), Positives = 131/249 (52%), Gaps = 9/249 (3%)

Query: 7   KTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIAD 66
           +  ++TGG  GIG A  RRFA EGAK  + D++    + +A  +      A  VRCD+ D
Sbjct: 21  RVCIVTGGAQGIGEACVRRFAAEGAKPVIVDVDDARGQALAAELG-----ALYVRCDVGD 75

Query: 67  RTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVL 126
           +  VDA +A      G +D+LVNNAG      F +    +++ ++ +NL G+  +  AV 
Sbjct: 76  KAQVDALVAQVLAAHGRIDVLVNNAGIFRAADFLEVTEADFDAVLRVNLKGSFLVGQAVA 135

Query: 127 PGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCPG 186
             MV    G IVN++S    +     A Y   KGG+   ++ +A   A   I VN V PG
Sbjct: 136 RAMVTSGGGAIVNMSSVNGVLAIPNIASYNVSKGGVNQLTRVMALALADKNIRVNAVAPG 195

Query: 187 PTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVLS 246
              T L A     +   ++ I + T   P+ RLG+P ++A  +A+  SD A ++TG++++
Sbjct: 196 TIATELAAKAVLTSDEAKRKIMSRT---PMKRLGQPSEIADVVAWLASDAASYVTGEIVT 252

Query: 247 VSGG-LTMN 254
           V GG +T+N
Sbjct: 253 VDGGRMTLN 261


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: 180
Number of extensions: 7
Number of successful extensions: 3
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: 267
Length adjustment: 25
Effective length of query: 230
Effective length of database: 242
Effective search space:    55660
Effective search space used:    55660
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 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