GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Shewanella halifaxensis HAW-EB4

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_012277951.1 SHAL_RS14880 enoyl-CoA hydratase

Query= BRENDA::D3RXI0
         (252 letters)



>NCBI__GCF_000019185.1:WP_012277951.1
          Length = 269

 Score =  115 bits (288), Expect = 9e-31
 Identities = 74/244 (30%), Positives = 128/244 (52%), Gaps = 9/244 (3%)

Query: 15  ARIKIANPPVNVLDMETMKEI---ISAIDEVEGVDVIVFSGEG-KSFSAGAEIK---EHF 67
           A I + NPP N    ++++E+   + A++E + V  +V + EG K FSAGA++K   +  
Sbjct: 25  AVISMNNPPANTWTAQSLQELKQKVLALNENKEVYALVITAEGDKFFSAGADLKLFADGD 84

Query: 68  PDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKLGVPEI 127
              A +M R+F +  + +     +++AA+ G+A+GGG E+A+ACD  +  + A++ +PE 
Sbjct: 85  KQNAADMARYFGEAFETLSTFHGVSIAAINGYAMGGGLEVALACDLRICEEQAQMALPEA 144

Query: 128 TLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFEESVNDF 186
           T+   P       L  ++G   A  +IL GE I AE+A +IGLV +V    N   +    
Sbjct: 145 TVGLLPCAGGTQNLTALVGEGWAKRMILCGERINAEKAEKIGLVEEVVVQGNAFNAAMAL 204

Query: 187 VNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKAFLEKRK 246
              +  +S  +++  K+ +          +  +  + Y + L  +ED  EG+ AFL KRK
Sbjct: 205 AEKVANQSPSSVKACKQLVQAGRSMPRSQVLPLERE-YFANLFDTEDQAEGVSAFLNKRK 263

Query: 247 PEWK 250
             WK
Sbjct: 264 ANWK 267


Lambda     K      H
   0.318    0.136    0.382 

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: 164
Number of extensions: 12
Number of successful extensions: 6
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: 252
Length of database: 269
Length adjustment: 24
Effective length of query: 228
Effective length of database: 245
Effective search space:    55860
Effective search space used:    55860
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 24 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