GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_02254
          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 (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