GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Dechlorosoma suillum PS

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate Dsui_2312 Dsui_2312 3-hydroxybutyrate dehydrogenase

Query= BRENDA::Q1J2J0
         (255 letters)



>FitnessBrowser__PS:Dsui_2312
          Length = 260

 Score =  127 bits (318), Expect = 3e-34
 Identities = 91/259 (35%), Positives = 132/259 (50%), Gaps = 23/259 (8%)

Query: 16  LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDV-GEGAARELDGTF------ER 68
           L G+ ALVTG   GIG  +AR LA+ GA V +    P    EG    +   F        
Sbjct: 2   LSGKIALVTGSTSGIGLAVARALARNGAAVMLNGSRPAAEAEGLRAAMAAEFGVKVAYTS 61

Query: 69  LNVTDADAVADLA----RRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWC 124
            ++ DA +V  LA    ++L  VD+LVNNAGI   A  ++ P++ W  ++++NL  VF  
Sbjct: 62  ADLADAASVRALAAAAEKQLGVVDILVNNAGIQHVAAVDEFPEEKWDQLIAINLSSVFHA 121

Query: 125 CREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVR 184
            +     M AR  G IV+ AS  GL+++    +A Y ASK AV+  ++++A E A  G+ 
Sbjct: 122 TKAVLPGMKARNWGRIVNIASAHGLVAS--PFKAPYTASKHAVVGFSKAVALEVAETGIT 179

Query: 185 VNAVAPGYTATPLTRRGL----------ETPEWRETWLKETPLGRLAEPREIAPAVLYLA 234
            NAV PGY  TPL  + +          E    R+  L   P  R  E  ++A  VL+L 
Sbjct: 180 CNAVCPGYVRTPLVEKQVAAQAKVHNLPEDQVIRDVILAAQPNKRFLEADDLAEFVLFLC 239

Query: 235 SDAASFVTGHTLVVDGGYT 253
           S A + +TG  L +DG +T
Sbjct: 240 SPAGAGMTGAALPMDGAWT 258


Lambda     K      H
   0.319    0.134    0.408 

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: 154
Number of extensions: 12
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: 260
Length adjustment: 24
Effective length of query: 231
Effective length of database: 236
Effective search space:    54516
Effective search space used:    54516
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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