GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Echinicola vietnamensis KMM 6221, DSM 17526

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate Echvi_2990 Echvi_2990 Acyl-CoA dehydrogenases

Query= BRENDA::Q39QF5
         (380 letters)



>FitnessBrowser__Cola:Echvi_2990
          Length = 402

 Score =  159 bits (402), Expect = 1e-43
 Identities = 111/374 (29%), Positives = 180/374 (48%), Gaps = 8/374 (2%)

Query: 5   TEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMG 64
           T E  L    +RD   +E++P   E  + + FP      F ++G   P +PA YGG  + 
Sbjct: 29  TAEHLLIRQSLRDFVKKEVSPYIEEWAQDAHFPSEIVPKFGEIGAFGPQIPAKYGGGGLD 88

Query: 65  VLTLALILEELGRVCASTALLLIAQTDGMLPIIHG-GSPELKERYLRRFAGESTLLTALA 123
            ++  LI++E+ R  +     +  Q   ++  IH  GS E +E++L + A     L    
Sbjct: 89  YISYGLIMQEIERGDSGMRSTVSVQGSLVMYPIHAFGSEEQREKFLPKLAS-GEWLGCFG 147

Query: 124 ATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAF 183
            TEP  GS+   + T     GD Y++NG K +I+N   AD+ VV+A  +  +    I   
Sbjct: 148 LTEPDHGSNPGGLTTSFKDNGDHYLLNGAKMWISNAPEADIAVVWAKDENGR----IHGL 203

Query: 184 VVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRV 243
           +VE+G  G        K  +R S   EL F+N++VP EN++  + +G +  +  L   R 
Sbjct: 204 IVERGMEGFTTPTTHHKWSLRASCTGELVFDNVKVPKENLLPGK-SGLSAPLMCLDAARY 262

Query: 244 FCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAE 303
             A  A+G A    + A R+  +R+QF KPIA    VQ  +A+M T +  ++LL  +   
Sbjct: 263 GIAWGAIGAAMDCYESAKRYAMERIQFDKPIAAFQLVQKKLAEMLTEITKAQLLAWRLGT 322

Query: 304 LLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYT 363
           L D G K      SMAK      A+ +  +A Q+ GG G   +  + R M + +    Y 
Sbjct: 323 LKDQG-KATSAQISMAKRNNVAMALEIAREARQIHGGMGITGDYPIMRHMMNLESVITYE 381

Query: 364 GTNQITRMVTGRAL 377
           GT+ I  ++ G+ +
Sbjct: 382 GTHDIHLLILGQEI 395


Lambda     K      H
   0.319    0.134    0.371 

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: 327
Number of extensions: 16
Number of successful extensions: 5
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: 380
Length of database: 402
Length adjustment: 31
Effective length of query: 349
Effective length of database: 371
Effective search space:   129479
Effective search space used:   129479
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 (21.7 bits)
S2: 50 (23.9 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