GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcdH in Caulobacter crescentus NA1000

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate CCNA_02254 CCNA_02254 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>lcl|FitnessBrowser__Caulo:CCNA_02254 CCNA_02254 isovaleryl-CoA
           dehydrogenase
          Length = 386

 Score =  201 bits (510), Expect = 4e-56
 Identities = 126/378 (33%), Positives = 197/378 (52%), Gaps = 2/378 (0%)

Query: 14  LDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYG 73
           +D  L +    +R+    +A  K+AP   +     +    ++  MG++GL G T+ E++G
Sbjct: 9   MDFALGETADAIRETTARFAADKIAPIAAKIDETNSFPRELWVPMGDLGLHGITVEEEFG 68

Query: 74  GPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWI 133
           G GL Y+ + +   EV R  +         S+L +  I  + +  QK +YLPKL +GE +
Sbjct: 69  GLGLGYLEHVVAMEEVSRASASVGLSYGAHSNLCVNQIRRWATPEQKARYLPKLISGEHV 128

Query: 134 GCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDEI 193
           G   ++E   GSD  SM  RA +V   Y L+G+K WITN+P AD  VV+AK  E  R  I
Sbjct: 129 GSLAMSEAGAGSDVVSMKLRAEQVGDRYILNGTKFWITNAPHADTLVVYAKTGEGSRG-I 187

Query: 194 RGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGP-FTCLNS 252
             FI+EKG KG S      K+G+R S T E+V ++  +PEEN++  V G  G   + L+ 
Sbjct: 188 TAFIVEKGMKGFSVSKKLDKMGMRGSDTAELVFEDCEIPEENVMGPVGGGVGVLMSGLDY 247

Query: 253 ARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLR 312
            R  +A G LG  ++C  +   YV DRKQFG+P+ + QL+Q K+ADM   +      V  
Sbjct: 248 ERAVLAAGPLGIMQACLDVVLPYVRDRKQFGQPIGSFQLMQGKIADMYVALNSARAYVYA 307

Query: 313 LGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNT 372
           + +  D G       +     +   A+ ++  A   LGG G + E+ V R L + ++ + 
Sbjct: 308 VAKACDAGKTTRFDAAGAILMASENAVKVSLEAIQALGGAGYTKEWPVERLLRDAKLYDI 367

Query: 373 YEGTHDIHALILGRAQTG 390
             GT++I   ++GR   G
Sbjct: 368 GAGTNEIRRFLIGRELIG 385


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: 341
Number of extensions: 15
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: 386
Length adjustment: 31
Effective length of query: 364
Effective length of database: 355
Effective search space:   129220
Effective search space used:   129220
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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