GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ch1CoA in Pseudomonas fluorescens FW300-N2E2

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate Pf6N2E2_5333 Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Query= SwissProt::Q2LQN9
         (414 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5333 Butyryl-CoA
           dehydrogenase (EC 1.3.99.2)
          Length = 378

 Score =  253 bits (645), Expect = 9e-72
 Identities = 151/372 (40%), Positives = 212/372 (56%), Gaps = 4/372 (1%)

Query: 40  EQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDIT 99
           E +L  + VR    +E  P   + ++         +   + G+L   +P  YGG   D  
Sbjct: 10  EHELFRDSVRTFLEKEAVPYHSQWEKQGHVDRQLWNKAGEAGMLCSHLPEAYGGLDADFL 69

Query: 100 TFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRFGEKSTLMTAFAAT 158
              +V+EEIG++   T +     +D +   IL  GS ALK KYLP+      ++TA A T
Sbjct: 70  YSTVVIEEIGRL-GLTGIGFSLHSDIVAPYILHYGSEALKHKYLPKL-VSGEMVTAIAMT 127

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

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

Query: 279 ASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATTLL 338
           A   +  A+ AL+  + +TRER+ FGK IA     +F +A+MATE++  R+ V +    L
Sbjct: 248 AIGGLASAEAALQWTLDYTRERKAFGKSIADFQNTRFKLAEMATEIQIGRVFVDRCLE-L 306

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

Query: 399 NQITRMVTGRSL 410
           N+I + +  RSL
Sbjct: 367 NEIMKEIIARSL 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: 358
Number of extensions: 16
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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