GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pontibacillus litoralis JSM 072002

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_036834462.1 N784_RS09610 acyl-CoA dehydrogenase

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



>NCBI__GCF_000775615.1:WP_036834462.1
          Length = 379

 Score =  235 bits (599), Expect = 2e-66
 Identities = 132/375 (35%), Positives = 212/375 (56%), Gaps = 5/375 (1%)

Query: 15  LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74
           ++ Q TEE+ M+R     FA  ++AP V +  + +     + ++MG++GL+G  IPEQYG
Sbjct: 1   MNLQFTEEQHMMRKMVRDFANKEVAPIVQQMDQEDYFPIELIKQMGDIGLMGIPIPEQYG 60

Query: 75  GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134
           GSG+++  Y +   E+ ++ +    ++SV +S+   PI  FGTE QKQKY+PKLASGE++
Sbjct: 61  GSGMDFPSYIIAIHELSKVSASVGVILSVHTSVGTNPILYFGTEEQKQKYIPKLASGEFL 120

Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAG----D 190
           G F LTEP  GSD GS+  +A +    Y L GSK++ITN   AD F+V+A+ D+      
Sbjct: 121 GAFALTEPGAGSDAGSLKMKAVREGEEYILNGSKVFITNGEKADTFIVFARTDSNAGNKG 180

Query: 191 IRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVP-EENIFPDVRGLKGPFTCLN 249
           +  F++E+   G        K+G+  S T  +  DN  +P E+ +  +  G K     LN
Sbjct: 181 VTAFIVERNTSGFEIGKKEHKMGMNGSGTVTLNFDNCRIPAEQRLGEEGEGFKIAMANLN 240

Query: 250 SARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCL 309
             R GI+  +LG AEA    A  Y  +R+QFG+P+A NQ I  KLADM T +  A     
Sbjct: 241 VGRIGIAAQSLGIAEAALEHAVGYAKEREQFGKPIARNQGISFKLADMATSVEAAKLLTY 300

Query: 310 RLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVN 369
               ++ +G    +  S+ K  +   A+++A  A  + GG G ++++ V R   + +V  
Sbjct: 301 HAANLRHQGIDCGKEASMAKMTASQAAMNVATEAIQVYGGYGYTEDYPVERFFRDAKVCE 360

Query: 370 TYEGTHDVHALILGR 384
            YEGT+++  +++G+
Sbjct: 361 IYEGTNEIQRVVIGK 375


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: 337
Number of extensions: 14
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: 379
Length adjustment: 30
Effective length of query: 363
Effective length of database: 349
Effective search space:   126687
Effective search space used:   126687
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 24 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