GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Herbaspirillum seropedicae SmR1

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate HSERO_RS02925 HSERO_RS02925 3-oxoacyl-ACP reductase

Query= BRENDA::Q8GR61
         (262 letters)



>FitnessBrowser__HerbieS:HSERO_RS02925
          Length = 244

 Score =  142 bits (358), Expect = 7e-39
 Identities = 85/261 (32%), Positives = 130/261 (49%), Gaps = 27/261 (10%)

Query: 2   SKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSY 61
           S  F   V +VTG  G IG A + RLA  G  + + D + +A     +  R++ +     
Sbjct: 7   SYDFGDCVAVVTGGHGGIGAAISARLAAGGAQVVVWDQHHDAA----SPYRQQSI----- 57

Query: 62  VCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAF 121
             D+T   AV+     ++ D G+IDFL NNAGY G   P+ +Y   ++ R++ +N+ G F
Sbjct: 58  --DITDAPAVMQAAQELLADTGRIDFLINNAGYAGPTVPLDEYDVGEWHRIVQVNLLGVF 115

Query: 122 HVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIR 181
           H  ++V+  M     GRIVN AS+AG +G PN +AY  +K  ++ALT++   +LA   + 
Sbjct: 116 HACRSVTPAMRAARRGRIVNIASLAGKEGTPNASAYSAAKAGVLALTKSLGKELAESGVL 175

Query: 182 VNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVV 241
           VNAI+P                A V +           Q MI   PM R G ++E+  + 
Sbjct: 176 VNAIAP----------------AAVKTALLGQMSPAHVQTMIAKSPMHRLGSVDEVADMC 219

Query: 242 AFLLGDDSSFMTGVNLPIAGG 262
           A+L     SF TG    ++GG
Sbjct: 220 AWLCSGSCSFNTGAVFDLSGG 240


Lambda     K      H
   0.318    0.135    0.384 

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: 150
Number of extensions: 8
Number of successful extensions: 3
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: 262
Length of database: 244
Length adjustment: 24
Effective length of query: 238
Effective length of database: 220
Effective search space:    52360
Effective search space used:    52360
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 17 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