GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Pseudomonas simiae WCS417

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate GFF814 PS417_04135 acyl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__WCS417:GFF814
          Length = 378

 Score =  261 bits (667), Expect = 2e-74
 Identities = 156/372 (41%), Positives = 217/372 (58%), Gaps = 4/372 (1%)

Query: 40  EQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDIT 99
           E +L  E VR    ++ AP     ++         +   + G+L   +P EYGG G D  
Sbjct: 10  EHELFRESVRTFLEKDAAPFHGHWEKQGYIDRRLWNKAGEAGMLCSHLPEEYGGLGADFL 69

Query: 100 TFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRFGEKSTLMTAFAAT 158
             A+V+EEI ++   T +     +D +   IL  GS ALK KYLP+      ++TA A T
Sbjct: 70  YSAVVIEEISRL-GLTGIGFSLHSDIVAPYILHYGSEALKHKYLPKL-ISGEMVTAIAMT 127

Query: 159 EPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTFVV 218
           EPGAGSDL  +KT AV  GD+YVING K FITNG +A+++ V A TDP  GAKG S F+V
Sbjct: 128 EPGAGSDLQGVKTTAVLDGDEYVINGSKTFITNGYLAELVIVVAKTDPKAGAKGTSLFLV 187

Query: 219 ERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRVFC 278
           E  TPG   G   +K+GM+    SELFF+D+ VP ENL+G+ G GFAYLM  L   R+  
Sbjct: 188 EADTPGFDKGKRLEKVGMKAQDTSELFFQDVRVPKENLLGQAGMGFAYLMQELPQERLTV 247

Query: 279 ASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATTLL 338
           A  A+  A+ ALE  +++TRER+ FGK IA     +F +A+MATE++  R+ V K    L
Sbjct: 248 AIGALSSAEAALEWTLEYTRERKAFGKAIADFQNTRFKLAEMATEIQIGRVFVDKCMA-L 306

Query: 339 DAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIYTGT 398
             + K       MAK +A+D   KV  + VQ+ GG G+M EY + R   +A++ +IY GT
Sbjct: 307 HLEGKLDVPTAAMAKYWATDLQCKVLDECVQLHGGYGFMWEYPIARAWADARVQRIYAGT 366

Query: 399 NQITRMVTGRSL 410
           N+I + +  R+L
Sbjct: 367 NEIMKEIIARAL 378


Lambda     K      H
   0.318    0.133    0.375 

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: 352
Number of extensions: 14
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: 414
Length of database: 378
Length adjustment: 31
Effective length of query: 383
Effective length of database: 347
Effective search space:   132901
Effective search space used:   132901
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: 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