GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Herbaspirillum seropedicae SmR1

Align BadH (characterized)
to candidate HSERO_RS02535 HSERO_RS02535 short-chain dehydrogenase

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



>FitnessBrowser__HerbieS:HSERO_RS02535
          Length = 249

 Score =  149 bits (377), Expect = 4e-41
 Identities = 93/255 (36%), Positives = 139/255 (54%), Gaps = 12/255 (4%)

Query: 4   LQNKTAVITGGGG--GIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVR 61
           L++K A+ITGG G  G+G +T R  A +GA+I + DL  + AE  AGA    G     + 
Sbjct: 3   LKDKVAIITGGAGQNGLGFSTARLMAAQGARIVILDL--ERAEP-AGAAARLGAQHLGLV 59

Query: 62  CDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHM 121
            D+ D+ + +AA A      G +DILVNNAG        +    +++R++ ++L G L+M
Sbjct: 60  ADVTDKAACEAAAAAVLKQFGRIDILVNNAGVTQPAKLLEITGKDYDRILDVSLRGTLYM 119

Query: 122 HHAVLPGMVERRHGRIVNIASDAARVGSS--GEAVYAACKGGLVAFSKTLAREHARHGIT 179
             AVLP M  ++ G IV I+S +A+ G    G   Y+A K G++  ++ +ARE    GI 
Sbjct: 120 SQAVLPAMQAQQSGSIVCISSVSAQRGGGILGGPHYSAAKAGVLGLARAMAREFGPQGIR 179

Query: 180 VNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGF 239
           VN + PG   T +  D+ S     E       + IPLGRLG PDD+ G   F  SD + +
Sbjct: 180 VNCITPGLISTDINKDILSAEKKAE-----IAQTIPLGRLGGPDDVGGVCVFLASDLSQY 234

Query: 240 ITGQVLSVSGGLTMN 254
            TG  L V+GG+ ++
Sbjct: 235 CTGVTLDVNGGMLIH 249


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: 178
Number of extensions: 13
Number of successful extensions: 4
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: 249
Length adjustment: 24
Effective length of query: 231
Effective length of database: 225
Effective search space:    51975
Effective search space used:    51975
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