GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Cupriavidus basilensis 4G11

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 RR42_RS36415 RR42_RS36415 3-hydroxy-2-methylbutyryl-CoA dehydrogenase

Query= SwissProt::O18404
         (255 letters)



>FitnessBrowser__Cup4G11:RR42_RS36415
          Length = 260

 Score =  241 bits (614), Expect = 1e-68
 Identities = 132/258 (51%), Positives = 173/258 (67%), Gaps = 10/258 (3%)

Query: 4   NAVSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKELGDKVVFVPVDVTSEK 63
           +  +++TGGASGLG ATA  LA  G  V L D+ + KG  VA+ELG   VF  V+VTSE 
Sbjct: 6   SVTAVITGGASGLGEATARALAAHGVRVALFDMNAEKGEAVARELGG--VFCQVNVTSEA 63

Query: 64  DVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRL-----EDFQRVININTVG 118
           +V A    A+   G+  + VNCAGT  A+KT +  K    ++     + F+R+I IN +G
Sbjct: 64  EVEAGFAKARAALGQERILVNCAGTGNAIKTASRAKEAPDQIRFFASDAFERIIQINLIG 123

Query: 119 TFNVI-RLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIA 177
           +F  + R +AG++  +   +DG RGVI+NTASVAA DGQ+GQAAYSASKA VVGMTLPIA
Sbjct: 124 SFRCLARSAAGMLTLDA--RDGDRGVIINTASVAAQDGQMGQAAYSASKAGVVGMTLPIA 181

Query: 178 RDLSTQGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAHLVQAIYEN 237
           RDLS +GIR+ TI PG+FNTP+L    E V+  LA S+PFP+RLG P E+A L   +  N
Sbjct: 182 RDLSGEGIRVNTIMPGIFNTPLLQGAQEHVKAALAASVPFPKRLGAPEEFASLALEMCRN 241

Query: 238 PLLNGEVIRIDGALRMMP 255
              NGE +R+DGA+RM P
Sbjct: 242 SYFNGEAVRLDGAIRMAP 259


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: 225
Number of extensions: 14
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: 255
Length of database: 260
Length adjustment: 24
Effective length of query: 231
Effective length of database: 236
Effective search space:    54516
Effective search space used:    54516
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 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