GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pseudomonas fluorescens GW456-L13

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate PfGW456L13_2591 Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2591
          Length = 387

 Score =  216 bits (550), Expect = 9e-61
 Identities = 133/375 (35%), Positives = 198/375 (52%), Gaps = 5/375 (1%)

Query: 15  LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74
           L+  L E   M+RD    F   ++APR  +          ++R+ G++GLLG T+PE+YG
Sbjct: 6   LNFALGETIDMLRDQVQSFVAKEIAPRAAQIDIDNLFPADLWRKFGDMGLLGITVPEEYG 65

Query: 75  GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134
           G+GL Y+ + +   E+ R  +         S+L +  IN  G   QK KYLPKL SGE I
Sbjct: 66  GAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGNHEQKSKYLPKLISGEHI 125

Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDD----AGD 190
           G   ++EPN GSD  SM  RA K    Y L GSK WITN P A+ +V++AK D       
Sbjct: 126 GALAMSEPNAGSDVVSMKLRADKRGDKYVLNGSKTWITNGPDANTYVIYAKTDLEKGPHG 185

Query: 191 IRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVR-GLKGPFTCLN 249
           I  F++E+ W+G S      K+G+R S T E+  D+V VPEENI   +  G+K   + L+
Sbjct: 186 ITAFIVERDWKGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGVLNGGVKVLMSGLD 245

Query: 250 SARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCL 309
             R  +S G  G  +AC      Y  DR+QFG+ +   QLIQ K+ADM T++  +     
Sbjct: 246 YERVVLSGGPTGIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNASRAYLY 305

Query: 310 RLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVN 369
            + +  + G    +  + +   S  +A  +A  A  +LGGNG  +EF   R L + ++  
Sbjct: 306 AVAQACERGETTRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPAGRLLRDAKLYE 365

Query: 370 TYEGTHDVHALILGR 384
              GT ++  +++GR
Sbjct: 366 IGAGTSEIRRMLIGR 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: 320
Number of extensions: 13
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: 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