GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Cupriavidus basilensis 4G11

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate RR42_RS26910 RR42_RS26910 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>FitnessBrowser__Cup4G11:RR42_RS26910
          Length = 393

 Score =  217 bits (552), Expect = 5e-61
 Identities = 133/380 (35%), Positives = 206/380 (54%), Gaps = 7/380 (1%)

Query: 14  LDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYG 73
           L+  L +D  M+R+    +AQ +LAPR  E  R +      +++MG++G+LG T+ E+YG
Sbjct: 7   LNFHLGEDIDMLRETVRNWAQAELAPRAAEIDRTDQFPMDAWKKMGDLGVLGITVAEEYG 66

Query: 74  GPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWI 133
           G  + Y+++ +   E+ R  +         S+L +  I   G+ AQK +YLPKL +G+WI
Sbjct: 67  GANMGYLAHMIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTAAQKARYLPKLVSGDWI 126

Query: 134 GCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDED-GRDE 192
           G   ++EPN GSD  SM  RA      Y L+G+KMWITN P  DV VV+AK + D G   
Sbjct: 127 GALAMSEPNAGSDVVSMKLRADFKGDHYVLNGTKMWITNGPDCDVLVVYAKTEPDLGARG 186

Query: 193 IRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVK-GLRGPFTCLN 251
           +  FI+EKG KG S      K+G+R S TGE+V  +  VP ENIL     G +   + L+
Sbjct: 187 MTAFIVEKGMKGFSVAQKLDKLGMRGSHTGELVFQDVEVPVENILGGENLGAKVLMSGLD 246

Query: 252 SARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVL 311
             R  ++ G +G  ++C  +   Y+ DRKQFG+ +   QLIQ K+ADM T +      + 
Sbjct: 247 YERAVLSGGPVGIMQACMDVITPYIHDRKQFGQSIGEFQLIQGKVADMYTTLQAARSYLY 306

Query: 312 RLGRM-----KDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVN 366
            +G+      KD      +  + +   +  KA  +A  +  +LGGNG  +E+ V R   +
Sbjct: 307 TVGKNLDSLGKDHVRQVRKDCAAVILYTAEKATWMAGESVQILGGNGYINEYPVGRLWRD 366

Query: 367 LEVVNTYEGTHDIHALILGR 386
            ++     GT +I  +++GR
Sbjct: 367 AKLYEIGAGTSEIRRMLIGR 386


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: 342
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: 395
Length of database: 393
Length adjustment: 31
Effective length of query: 364
Effective length of database: 362
Effective search space:   131768
Effective search space used:   131768
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