GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Dechlorosoma suillum PS

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate Dsui_0975 Dsui_0975 acyl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>FitnessBrowser__PS:Dsui_0975
          Length = 390

 Score =  190 bits (483), Expect = 5e-53
 Identities = 126/372 (33%), Positives = 192/372 (51%), Gaps = 13/372 (3%)

Query: 24  MVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDYVSYG 83
           M+RD   A+A  ++APR  +  R     A ++++ G++GLLG T  E+YGG  + Y+++ 
Sbjct: 16  MLRDTVRAFAAKEIAPRAAQIDRDNEFPADLWQKFGDLGLLGMTAEEEYGGTAMGYLAHI 75

Query: 84  LIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTEPNH 143
           +   E+ R  +         S+L +  I   G+ AQK KYLP L +G  +G   ++EPN 
Sbjct: 76  VAMEEISRASASVGLSYGAHSNLCVNQIRRNGTAAQKAKYLPGLISGTQVGALAMSEPNA 135

Query: 144 GSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD-EDGRDEIRGFILEKGC 202
           GSD  SM  +A K    Y L+GSKMWITN   AD  VV+AK D   G   +  FI+EKG 
Sbjct: 136 GSDVVSMKLKAEKKGDRYVLNGSKMWITNGGDADTLVVYAKTDLNAGAKGMTAFIVEKGF 195

Query: 203 KGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHV-KGLRGPFTCLNSARYGIAWGA 261
           KG S      K+G+R S T  +  D+  VPEEN+L  V  G +   + L+  R  +  G 
Sbjct: 196 KGFSHGTHLDKLGMRGSNTFPLFFDDCEVPEENVLGGVGNGAKVLMSGLDYERAVLCGGP 255

Query: 262 LGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMKDEGT 321
           LG   +C  +   Y+ +R+QFG  +   QL+Q KLADM +        V  +G+  D   
Sbjct: 256 LGIMAACMDVVLPYLHEREQFGTAIGEFQLMQGKLADMYSTWQATRAYVYAVGQACDRAD 315

Query: 322 AAVEITSIMKRNSCG-------KALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYE 374
            A      +++++ G       KA  +A  A   LGG G ++E+   R   + ++     
Sbjct: 316 HA----RSLRKDAAGAILYSAEKATWMAGDAIQTLGGVGYTNEYPTGRLWRDAKLYEIGA 371

Query: 375 GTHDIHALILGR 386
           GT +I  +++GR
Sbjct: 372 GTSEIRRMLIGR 383


Lambda     K      H
   0.320    0.138    0.414 

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: 362
Number of extensions: 17
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: 395
Length of database: 390
Length adjustment: 31
Effective length of query: 364
Effective length of database: 359
Effective search space:   130676
Effective search space used:   130676
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