GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Rhodococcus qingshengii djl-6-2

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_050655857.1 C1M55_RS09530 acyl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>NCBI__GCF_002893965.1:WP_050655857.1
          Length = 380

 Score =  189 bits (480), Expect = 1e-52
 Identities = 121/380 (31%), Positives = 189/380 (49%), Gaps = 6/380 (1%)

Query: 12  LLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQ 71
           L+  Q+  D   + RD A       LAP+V E  + E     +F  +G+ GLL    PE+
Sbjct: 6   LMPSQEARDLIELTRDVADKV----LAPKVNEYEKAEKYPDGVFPALGQAGLLSLPYPEE 61

Query: 72  YGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGE 131
           +GG    Y  Y  +  E+    +     +SV S L   P+F FG+D QK ++LP +  G 
Sbjct: 62  FGGGDQPYEVYLQVLEEIASRWAAVAVAVSVHS-LSCFPLFTFGTDEQKNRWLPDMLGGN 120

Query: 132 WIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRD 191
            IG + L+E   GSD  ++  +A    GGY ++GSK WITN   AD + ++A+  +DG  
Sbjct: 121 TIGAYSLSEAQAGSDAAALSCKATPTDGGYRVNGSKAWITNGGKADFYNLFARTSDDGSR 180

Query: 192 EIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCL 250
            +   +++K  +GLS      K+GLRA  T     D+AF+PEE ++    +GL   F+ L
Sbjct: 181 GVSCLLVDKDAEGLSFGKPEEKMGLRAVPTASANYDDAFIPEERLIGQRGQGLPIAFSAL 240

Query: 251 NSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGV 310
           +S R GIA  A+G A+     A  Y  +RK FG+ +  +Q +   LADM   +       
Sbjct: 241 DSGRLGIAAVAVGIAQGALDDAVAYAKERKAFGKRIIDHQGLGFVLADMAAAVDSARATY 300

Query: 311 LRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVV 370
           L   R +D G       S+ K  +   A+ +   A  + GG G + +F V R++   ++ 
Sbjct: 301 LDAARRRDAGVPYSRNASVAKLVATDAAMKVTTDAVQVFGGYGYTQDFPVERYMREAKIT 360

Query: 371 NTYEGTHDIHALILGRAQTG 390
             +EGT+ I  L++ R   G
Sbjct: 361 QIFEGTNQIQRLVIARQLAG 380


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: 388
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: 395
Length of database: 380
Length adjustment: 30
Effective length of query: 365
Effective length of database: 350
Effective search space:   127750
Effective search space used:   127750
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