GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pseudomonas putida KT2440

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate PP_4064 PP_4064 isovaleryl-CoA dehydrogenase

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>FitnessBrowser__Putida:PP_4064
          Length = 387

 Score =  219 bits (558), Expect = 1e-61
 Identities = 136/376 (36%), Positives = 202/376 (53%), Gaps = 7/376 (1%)

Query: 15  LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPA-IFREMGEVGLLGATIPEQY 73
           L+  L E   M+RD    F   +LAPR  +   H+   PA ++R+ G++GLLG T+PE+Y
Sbjct: 6   LNFALGETIDMLRDQVRTFVAAELAPRAAQ-IDHDNLFPADMWRKFGDMGLLGITVPEEY 64

Query: 74  GGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEW 133
           GG+GL Y+ + +   E+ R  +         S+L +  IN  GT  QK KYLPKL SGE 
Sbjct: 65  GGAGLGYLAHVVSMEEISRGSASVALSYGAHSNLCVNQINRNGTHEQKLKYLPKLISGEH 124

Query: 134 IGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDD----AG 189
           IG   ++EPN GSD  SM  RA K    Y L GSK WITN P A+ +V++AK D    A 
Sbjct: 125 IGALAMSEPNAGSDVVSMKLRAEKRGDHYVLNGSKTWITNGPDANTYVIYAKTDLDKGAH 184

Query: 190 DIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVR-GLKGPFTCL 248
            I  F++E+ W+G S      K+G+R S T E+  D V VP ENI   +  G++   + L
Sbjct: 185 GITAFIVERDWKGFSRSNKFDKLGMRGSNTCELFFDGVEVPAENILGQLNGGVRVLMSGL 244

Query: 249 NSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGC 308
           +  R  +S G  G  ++C      Y  DR+QFG+ +   QLIQ K+ADM T++  +    
Sbjct: 245 DYERVVLSGGPTGIMQSCMDLVVPYIHDRKQFGQSIGEFQLIQGKIADMYTQLNASRAYL 304

Query: 309 LRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVV 368
             + +  D G    +  + +   +  +A  +A  A  +LGGNG  +EF   R L + ++ 
Sbjct: 305 YAVAQACDRGETTRKDAAGVILYTAERATQMALEAIQILGGNGYINEFPAGRLLRDAKLY 364

Query: 369 NTYEGTHDVHALILGR 384
               GT ++  +++GR
Sbjct: 365 EIGAGTSEIRRMLIGR 380


Lambda     K      H
   0.320    0.137    0.413 

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: 329
Number of extensions: 11
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: 393
Length of database: 387
Length adjustment: 31
Effective length of query: 362
Effective length of database: 356
Effective search space:   128872
Effective search space used:   128872
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: 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