GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Desulfacinum infernum DSM 9756

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_073037627.1 BUB04_RS05240 glutaryl-CoA dehydrogenase Acd

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



>NCBI__GCF_900129305.1:WP_073037627.1
          Length = 385

 Score =  216 bits (549), Expect = 1e-60
 Identities = 128/379 (33%), Positives = 206/379 (54%), Gaps = 6/379 (1%)

Query: 18  QLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSG 77
           +LTEE+++V++ A +FA++++ P + E  +    +    R+MGE+G  G  IPE+YGG+G
Sbjct: 4   ELTEEQKIVQEQARRFAENEILPTLEEEEKGHVFNRERLRKMGELGFFGCAIPEEYGGNG 63

Query: 78  LNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCF 137
           + +V   L+  ++ ++   +R   ++Q+    + +N+FGTE QK+ Y+P   SGE +G F
Sbjct: 64  MGFVESVLMTEQIAKVSPSWRVPFNMQNIGPAITVNQFGTEEQKRAYIPGWVSGEKVGFF 123

Query: 138 GLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDA----GDIRG 193
            +TEPN GSD   M T A+ +   + L G KMWI+N+PIADV +V+A  D       +  
Sbjct: 124 AITEPNAGSDVAGMRTTAKDMGDHWELNGQKMWISNAPIADVGLVYAYTDKEKKYKGMTC 183

Query: 194 FVLE-KGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDV-RGLKGPFTCLNSA 251
           F+++  G   +   AI  K+GL  S TGEI+ D   +P++ +   V  G K     LN+ 
Sbjct: 184 FIVDVAGNPNIVTRAIESKLGLHCSPTGEIIFDGAKIPKDAVLGQVGDGFKICMWMLNNT 243

Query: 252 RYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRL 311
           R   + GALG + AC   A +Y  +R QFG+P++  Q+IQ ++A+M  E   A       
Sbjct: 244 RISCAAGALGVSGACLDLAVKYANERTQFGKPISTYQMIQAQIAEMAAEHEAAKWLVYHA 303

Query: 312 GRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTY 371
             +KD+G      TSI K  +   A+  A  A  + G  G S E+ + R   + +     
Sbjct: 304 AYLKDQGKPNQLQTSIAKYYASEAAVRAANEAMKIFGSYGFSTEYPIERFYRDAKSYQIV 363

Query: 372 EGTHDVHALILGRAQTGIQ 390
           EGT +V  +I+     G Q
Sbjct: 364 EGTSNVQKMIIAGITCGHQ 382


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: 359
Number of extensions: 16
Number of successful extensions: 3
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: 385
Length adjustment: 30
Effective length of query: 363
Effective length of database: 355
Effective search space:   128865
Effective search space used:   128865
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 Apr 09 2024. 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