GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Desulfovibrio vulgaris Miyazaki F

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 8502147 DvMF_2858 short-chain dehydrogenase/reductase SDR (RefSeq)

Query= BRENDA::Q1J2J0
         (255 letters)



>FitnessBrowser__Miya:8502147
          Length = 245

 Score = 89.7 bits (221), Expect = 5e-23
 Identities = 81/247 (32%), Positives = 106/247 (42%), Gaps = 21/247 (8%)

Query: 19  RHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFERLNVTDADAVA 78
           R+A+VTGG++GIG  IA  LAQ G  V +   N      AA E+     R         A
Sbjct: 6   RNAIVTGGSRGIGRAIALRLAQDGFCVVV---NYASNAPAALEVVDAIARTGGQAVAVPA 62

Query: 79  DLARR-------------LPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCC 125
           D+                   V V+VN+AGI+   P        +  VL  NL G F   
Sbjct: 63  DVGETGDVEGLFAAAHDAFGQVGVVVNSAGIMPMLPIAGGDTAAFEKVLRTNLTGTFNVL 122

Query: 126 REFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185
                 + A GR   +ST+ ++     +      Y ASKA V  L R LA E   R + V
Sbjct: 123 SRAANALTAGGRIIALSTSVIAKPFPGY----GPYIASKAGVEGLVRVLANELRGRSITV 178

Query: 186 NAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHT 245
           NAVAPG  AT L   G +T E      K  PL RL  P EIA  V +L      ++    
Sbjct: 179 NAVAPGPVATDLFLNG-KTEEQIAAIGKLAPLERLGTPEEIAGVVSFLVGPEGGWINAQV 237

Query: 246 LVVDGGY 252
           + V+GG+
Sbjct: 238 VRVNGGF 244


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: 181
Number of extensions: 8
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: 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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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