GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Rhizobium leguminosarum bv. trifolii WSM1325

Align 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)
to candidate WP_012760743.1 RLEG_RS35145 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::O18404
         (255 letters)



>NCBI__GCF_000023185.1:WP_012760743.1
          Length = 255

 Score =  268 bits (684), Expect = 1e-76
 Identities = 138/253 (54%), Positives = 176/253 (69%), Gaps = 2/253 (0%)

Query: 1   MIKNAVSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKELGDKVVFVPVDVT 60
           +I+ A  +VTGG SGLG AT   L + G  V +ADL +  G E+A+E G    FV  DVT
Sbjct: 2   LIRGASFIVTGGGSGLGAATVRALVEAGGRVTIADLNAEAGQEIAREFGSDACFVKADVT 61

Query: 61  SEKDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGTF 120
             ++ +A +  A + FG L   VNCAG A A K     ++  HRLE F R + IN +GTF
Sbjct: 62  DGEEGAAVVAAAVEAFGSLRGLVNCAGVAPAEKVIG--RDGPHRLESFARTVGINLIGTF 119

Query: 121 NVIRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDL 180
           N+IRL+A  +   EP+ +G+RGVIVNTASVAAFDGQIGQAAY+ASK  V  MTLPIAR+L
Sbjct: 120 NMIRLAAAAIQTTEPDAEGERGVIVNTASVAAFDGQIGQAAYAASKGGVAAMTLPIAREL 179

Query: 181 STQGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAHLVQAIYENPLL 240
           +  GIR+  IAPG+F TPM+A +P +V+  L KS+PFP RLG P+E+A LV+ I EN +L
Sbjct: 180 ARHGIRVVAIAPGIFETPMMADMPAEVQAALGKSVPFPPRLGRPAEFAGLVRHILENNML 239

Query: 241 NGEVIRIDGALRM 253
           NGEVIR+DGALRM
Sbjct: 240 NGEVIRLDGALRM 252


Lambda     K      H
   0.317    0.133    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: 245
Number of extensions: 10
Number of successful extensions: 2
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: 255
Length of database: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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