GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudarthrobacter sulfonivorans Ar51

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_058929014.1 AU252_RS00320 3-hydroxyacyl-CoA dehydrogenase family protein

Query= BRENDA::C4IEM5
         (282 letters)



>NCBI__GCF_001484605.1:WP_058929014.1
          Length = 292

 Score =  194 bits (494), Expect = 1e-54
 Identities = 112/280 (40%), Positives = 161/280 (57%), Gaps = 3/280 (1%)

Query: 3   KVFVLGAGTMGAGIVQAFAAKGCEVIVRDIKEEFVDRGIATITKSLSKLVAKEKITEADK 62
           +V VLG G MGAGI  AF   G +V+V +  E     G   +  S +K +  E+    + 
Sbjct: 13  RVGVLGGGRMGAGIAHAFLIIGADVVVVERDEASAQAGRERVKSSAAKSI--ERNPGGNL 70

Query: 63  EEILSRISGTTDMKLAADCDLVVEAAIENMKIKKEIFAELDGICKPETILASNTSSLSIT 122
           +E++SR+S + D    AD +LVVEA  E+  +K      ++    P T+LASNTSSLS++
Sbjct: 71  DEMVSRLSVSVDYAAFADRELVVEAVPEDWDLKVTALRRVEEQLTPGTVLASNTSSLSVS 130

Query: 123 EVASATKRADKVIGMHFFNPAPVMKLVEVIRGAATSQETFDAVKEMSESIGKTPVEVAEA 182
            +A    R    +GMHFFNP P   L+EV+ G  T  E  +  +     +GKT V V +A
Sbjct: 131 GLAEELARPQDFLGMHFFNPVPASTLIEVVIGKQTRPELVEQARSWVHGLGKTAVVVNDA 190

Query: 183 PGFVVNRILIPMINEATFILQEGVAKEEDIDAAMKLGANHPMGPLALGDLIGLDVCLAIM 242
           PGF  +R+ + +  EA  +++EGVA  +DID AM LG  HP GPL   D++GLDV L I 
Sbjct: 191 PGFASSRLGVAIALEAMRMVEEGVASAKDIDNAMVLGYKHPTGPLRTTDIVGLDVRLGIA 250

Query: 243 DVLYNETGDTKYRASSLLRKYVRAGWLGRKTGKGFYDYSK 282
             L+   G+ ++    +LR  V  G LGRKTGKGF+D+++
Sbjct: 251 TYLHETLGE-RFAPPQILRDKVARGELGRKTGKGFFDWTQ 289


Lambda     K      H
   0.317    0.134    0.369 

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: 208
Number of extensions: 5
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: 282
Length of database: 292
Length adjustment: 26
Effective length of query: 256
Effective length of database: 266
Effective search space:    68096
Effective search space used:    68096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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