GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Dyadobacter tibetensis Y620-1

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_044199233.1 X939_RS0111485 glucose 1-dehydrogenase

Query= SwissProt::O18404
         (255 letters)



>NCBI__GCF_000566685.1:WP_044199233.1
          Length = 249

 Score =  117 bits (292), Expect = 3e-31
 Identities = 81/254 (31%), Positives = 126/254 (49%), Gaps = 16/254 (6%)

Query: 1   MIKNAVSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAK---ELGDKVVFVPV 57
           +++N ++LVTG  SG+G + A   A QGA V+++     KGN V K   E G    F+  
Sbjct: 2   LLQNKIALVTGATSGIGESIAILFAAQGAKVVVSGRNHEKGNSVVKKIKEAGGTATFLAA 61

Query: 58  DVTSEKDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTV 117
           +++        ++     +GRLD+  N AG    +          +  E++++VI+ N  
Sbjct: 62  EMSDSLQCKQLIEETVKIYGRLDIACNNAGLVEPLAPV-----ADYPEENWEKVISANLN 116

Query: 118 GTFNVIRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIA 177
           G F  ++    +M      Q G    I+N +SV    G+ G ++Y ASK  V G+T   A
Sbjct: 117 GVFYCLKYQLKVM-----LQHGGPCSIINMSSVLGQTGEKGLSSYIASKHGVNGLTKSAA 171

Query: 178 RDLSTQGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAHLV--QAIY 235
            + +T GIRI  + P    TP+LA LPE+ R  L  + P  +RLG+P E A LV   A  
Sbjct: 172 LENATNGIRINAVGPAYVETPILAVLPEETRKVLGSAQPM-ERLGQPEEIAELVLWLASD 230

Query: 236 ENPLLNGEVIRIDG 249
           ++  + G    IDG
Sbjct: 231 KSSFVTGSYYAIDG 244


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: 137
Number of extensions: 6
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: 249
Length adjustment: 24
Effective length of query: 231
Effective length of database: 225
Effective search space:    51975
Effective search space used:    51975
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