GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Dokdonella koreensis DS-123

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_067650170.1 I596_RS15900 3-oxoacyl-ACP reductase FabG

Query= SwissProt::O18404
         (255 letters)



>NCBI__GCF_001632775.1:WP_067650170.1
          Length = 243

 Score = 87.0 bits (214), Expect = 3e-22
 Identities = 81/252 (32%), Positives = 126/252 (50%), Gaps = 25/252 (9%)

Query: 8   LVTGGASGLGRATAERLAKQGASVIL-----ADLPSSKGNEVAKELGDKVVFVPVDVTSE 62
           LVTG + G+G+A A RLA+ G  ++L      D  ++   ++A  LG  V  +  DV   
Sbjct: 7   LVTGSSRGIGKAIALRLARDGYDLVLHCRSRLDEATAVAADIAA-LGRGVRVLQFDVGDR 65

Query: 63  KDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGTFNV 122
              +AAL    +  G     V  AG A        N   A   ED+  V++ N  G +NV
Sbjct: 66  AAAAAALLADVEAHGCPYGVVCNAGIARD------NAFPAMPPEDWDAVVHTNLDGFYNV 119

Query: 123 IR-LSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDLS 181
           +  L+  L+   +P      G IV  ASV+   G  GQ  YSA+KA ++G T  +A +L+
Sbjct: 120 LHPLTMPLVRRRKP------GRIVTLASVSGIIGNRGQVNYSAAKAGIIGATKALAVELA 173

Query: 182 TQGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAHLVQAIY--ENPL 239
           ++ I +  +APGL +T M+ A   +V     K+IP   R+G+P+E A LV  +   +   
Sbjct: 174 SRAITVNCVAPGLIDTEMVDA---RVLDEALKAIP-AGRVGKPAEVAALVSFLMGEDAAY 229

Query: 240 LNGEVIRIDGAL 251
           +  +VI ++G L
Sbjct: 230 ITRQVISVNGGL 241


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: 143
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: 243
Length adjustment: 24
Effective length of query: 231
Effective length of database: 219
Effective search space:    50589
Effective search space used:    50589
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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