GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_2816 Ga0059261_2816 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= SwissProt::O18404
         (255 letters)



>FitnessBrowser__Korea:Ga0059261_2816
          Length = 259

 Score =  229 bits (584), Expect = 4e-65
 Identities = 129/251 (51%), Positives = 165/251 (65%), Gaps = 7/251 (2%)

Query: 7   SLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKELGDKVVFVPVDVTSEKDVS 66
           ++VTGGASGLG ATA+ +A+ GA V + DL    G +VA E+G   +F  VDV S++ V 
Sbjct: 9   AIVTGGASGLGHATAKAIAETGAKVAIFDLNEELGEKVAAEIGG--IFCKVDVLSDESVD 66

Query: 67  AALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAH----RLEDFQRVININTVGTFNV 122
           AA + A+   G+  + VNCAGT  ++KT   +K          + F  V+ +NTVGTF  
Sbjct: 67  AAFEKARSANGQERVLVNCAGTGNSIKTAGVDKKTGEIKYFPSDKFAWVLMVNTVGTFRC 126

Query: 123 IRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDLST 182
           I  SA  M   +P  DG+RG IV TAS AA DGQ+GQAAYSASKAAVVGMTLPIARDLS 
Sbjct: 127 ITRSAAGMLTLDP-VDGERGAIVCTASAAAQDGQMGQAAYSASKAAVVGMTLPIARDLSG 185

Query: 183 QGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAHLVQAIYENPLLNG 242
             IRI TI PG+F TP +  +P+ VR+ L  S+PFP+R G P+EYA LV  +  N   NG
Sbjct: 186 SAIRINTIMPGIFATPPMLGVPDNVRSVLEASVPFPKRFGAPAEYASLVLEMVRNGYFNG 245

Query: 243 EVIRIDGALRM 253
           E +R+DGA+RM
Sbjct: 246 ETVRLDGAIRM 256


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: 215
Number of extensions: 12
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: 259
Length adjustment: 24
Effective length of query: 231
Effective length of database: 235
Effective search space:    54285
Effective search space used:    54285
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