GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Algiphilus aromaticivorans DG1253

Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_043765518.1 U743_RS03380 acyl-CoA dehydrogenase

Query= BRENDA::P12007
         (424 letters)



>NCBI__GCF_000733765.1:WP_043765518.1
          Length = 381

 Score =  185 bits (470), Expect = 2e-51
 Identities = 120/378 (31%), Positives = 202/378 (53%), Gaps = 11/378 (2%)

Query: 43  LNEEQKQLRHTISKFVQENLAPKAQEIDQSNDFKNLREFWKQLGSLGVLGITAPVQYGGS 102
           LN E + +R  +++FV+  + P     +++ +    R   K     GVL I  P   GG 
Sbjct: 8   LNAEHEAIRDQVARFVEREITPNIDAWEEAGELP--RALHKAAAEAGVLQIGYPEALGGI 65

Query: 103 GL-GYLEHVLVMEEISRASAAVGLSYGAHSN-LCINQIVRNGNEAQKEKYLPKLISGEFI 160
            +  +   ++++EE+ RA +  GL  G  S+ + +  IV  G + QKE+ +  +++G+ I
Sbjct: 66  DVPDHFYELVIVEELCRAGSG-GLIAGLMSHGIGLPPIVAAGTQEQKERLVAPVLAGDKI 124

Query: 161 GALAMSEPNAGSDVVSMRLKAEKKGDHYVLNGNKFWITNGPDADVLVVYAKTDLTAVPAS 220
            AL ++EP+ GSDV ++R  A ++G+HY++ G+K +IT+G  ADV+    +T    +   
Sbjct: 125 AALGITEPSGGSDVAAIRTAARREGNHYIVKGSKTFITSGMRADVITTAVRTGGEGI--- 181

Query: 221 RGITAFIVEKDMPGFSTSKKLDKLGMRGSNTCELVFEDCKVPAANILSQESKGVYVLMSG 280
            GI+   VE D PG S +  LDK+G R S+T  L F++ +VP AN++  E+ G   +M  
Sbjct: 182 GGISLLAVEADTPGLSRT-PLDKMGWRCSDTATLYFDEARVPVANLIGPENAGFMAIMQN 240

Query: 281 LDLERLVLAGGPLGIMQAVLDHTIPYLHVREAFGQKIGQFQLMQGKMADMYTRLMACRQY 340
            + ERL LA    G+ +   +  + +   RE FG+ +   Q+++ K+ DM   + A    
Sbjct: 241 FNSERLGLAAQAWGLAKTCYEEALTWARERETFGKPLIARQVIRHKLVDMKMAIDAVGAQ 300

Query: 341 VYNVA-RACDEGHITAKDCAGVILYTAECATQVALDGIQCLGGNGYINDFPMGRFLRDAK 399
           +Y +A R   + +  A+ C    L T+    QVA + +Q LGG GY+      R  R+ K
Sbjct: 301 LYQLAWRVSQKQYPVAELCMLKNLATS-TLEQVAGEAVQILGGAGYLRGAKSERIFRETK 359

Query: 400 LYEIGGGTSEVRRLVIGR 417
           +  IGGG SEV + +  R
Sbjct: 360 VLSIGGGASEVMKDLAAR 377


Lambda     K      H
   0.320    0.137    0.402 

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: 353
Number of extensions: 19
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: 424
Length of database: 381
Length adjustment: 31
Effective length of query: 393
Effective length of database: 350
Effective search space:   137550
Effective search space used:   137550
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