GapMind for catabolism of small carbon sources

 

Alignments for a candidate for had in Cupriavidus basilensis 4G11

Align 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase; EC 1.1.1.368 (characterized)
to candidate RR42_RS34260 RR42_RS34260 alcohol dehydrogenase

Query= SwissProt::O87871
         (368 letters)



>FitnessBrowser__Cup4G11:RR42_RS34260
          Length = 342

 Score =  113 bits (283), Expect = 7e-30
 Identities = 100/345 (28%), Positives = 147/345 (42%), Gaps = 25/345 (7%)

Query: 27  GAPMVRAEFEIGELSADQVVVAVAGCGVCHTDLGYYYDSVRTNHALPLALGHEISGRVVQ 86
           GAP+   E  + +    Q+ V +   GVCHTDL            LP   GHE  G V  
Sbjct: 14  GAPLTIDEVPVPQPGRGQIQVKIEASGVCHTDLHAAEGDWPVKPTLPFIPGHEGVGYVSA 73

Query: 87  AGANAAQWL-GRAVIVPAVMP-CGTCELCTSGHGTICRDQVMPGNDIQGGFASHVVVPAR 144
            GA  ++   G  V VP +   CG CE C  G  T+C  Q   G  + GG+  +VV    
Sbjct: 74  VGAGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQQNTGYSVNGGYGEYVVADPN 133

Query: 145 --GLCPVDEARLAAAGLQLADVSVVADAVTTPYQAVLQAGVEPGDVAVVIGVGGVGGYAV 202
             GL P     +  A +  A V+V        Y+ +      PG   V+ G+GG+G  AV
Sbjct: 134 YVGLLPDSVGFVEIAPILCAGVTV--------YKGLKVTDTRPGQWVVISGIGGLGHVAV 185

Query: 203 QIANAFGASVVAIDVDPAKLEMMSKHGAALTLNAREISG-RDLKKAIEAHAKANGLRLTR 261
           Q A A G  V A+D+D  KLE+  K GA +T+NAR       L+K I     A+G  +T 
Sbjct: 186 QYARAMGLRVAAVDIDDKKLELARKLGAEVTVNARTTDPVAFLQKEI---GGAHGALVT- 241

Query: 262 WKIFECSGTGAGQTSAYGLLTHGATLAVVGFTMDKVEVRLSNLMAFHARALGNWGCLPEY 321
                 S    GQ  A G++  G T+A+ G         + +++       G+       
Sbjct: 242 ----AVSPKAFGQ--AIGMVRRGGTIALNGLPPGDFPTPIFDVVLKGITIRGSIVGTRSD 295

Query: 322 YPAALDLVLDKKIDLASFIERHPLDQIGEVFAAAHAHKLTRRAIL 366
              +LD      +   + +   PL++I E+F    A  +  R ++
Sbjct: 296 LQESLDFAAHGAV--KATVSTAPLEKINEIFTRMRAGDIEGRVVM 338


Lambda     K      H
   0.320    0.134    0.406 

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: 293
Number of extensions: 18
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: 368
Length of database: 342
Length adjustment: 29
Effective length of query: 339
Effective length of database: 313
Effective search space:   106107
Effective search space used:   106107
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: 49 (23.5 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