GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Burkholderia phytofirmans PsJN

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate BPHYT_RS23260 BPHYT_RS23260 isovaleryl-CoA dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS23260
          Length = 393

 Score =  222 bits (565), Expect = 2e-62
 Identities = 140/378 (37%), Positives = 202/378 (53%), Gaps = 14/378 (3%)

Query: 19  LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGL 78
           L EE  M+RDS   FA  ++APR  E  R +Q    ++R+ G++G+LG T+ E+YGG+ +
Sbjct: 11  LGEEIEMLRDSIAGFAAKEIAPRAAEIDRTDQFPMDLWRKFGDLGVLGMTVSEEYGGANM 70

Query: 79  NYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFG 138
            Y  + +   E+ R  +         S+L +  I+  GTEAQKQKYLPKL SGE +G   
Sbjct: 71  GYTAHMIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEAQKQKYLPKLVSGEHVGALA 130

Query: 139 LTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDD----AGDIRGF 194
           ++EPN GSD  SM  RA K    Y L G+KMWITN P  D  VV+AK D    +  I  F
Sbjct: 131 MSEPNAGSDVVSMKLRAEKKGDHYVLNGTKMWITNGPDCDTLVVYAKTDPEANSRGITAF 190

Query: 195 VLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVR-GLKGPFTCLNSARY 253
           ++EKG +G S      K+G+R S TGE+V  +V VPEENI   +  G K   + L+  R 
Sbjct: 191 IVEKGMKGFSVAQKLDKLGMRGSHTGELVFQDVEVPEENILGQLNGGAKVLMSGLDYERA 250

Query: 254 GISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGR 313
            ++ G  G   A       Y  DR+QFG+ +   QLIQ K+AD+ T +         +GR
Sbjct: 251 VLAGGPTGIMVAVMDAVVPYIHDRKQFGQSIGEFQLIQGKVADLYTTLQACRAYLYAVGR 310

Query: 314 MKDEGTAAVEITSIMKRNSCG-------KALDIARMARDMLGGNGISDEFGVARHLVNLE 366
             D  T   E    ++++  G       KA  +A  A  +LGGNG  +E+ V R   + +
Sbjct: 311 QLD--TLGKEHVRQVRKDCAGVILYTAEKATWMAGEAIQILGGNGYINEYPVGRLWRDAK 368

Query: 367 VVNTYEGTHDVHALILGR 384
           +     GT ++  +++GR
Sbjct: 369 LYEIGAGTSEIRRMLIGR 386


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: 345
Number of extensions: 12
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: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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