GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Sphingomonas koreensis DSMZ 15582

Align 3-hydroxypropanonate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate Ga0059261_3686 Ga0059261_3686 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)

Query= metacyc::MONOMER-18957
         (354 letters)



>FitnessBrowser__Korea:Ga0059261_3686
          Length = 295

 Score =  121 bits (303), Expect = 3e-32
 Identities = 97/322 (30%), Positives = 148/322 (45%), Gaps = 32/322 (9%)

Query: 20  GFIGLGLMGQHMARHVYNQLEPSDKLYVYDVDPKHTTQFLTEVTSQTPQNAPLLTPLNSL 79
           GFIGLG MG  MA    N  +    +  +D+      +            A    P+ S 
Sbjct: 5   GFIGLGNMGGGMAA---NLAKAGHDVRAFDLSADALER----------AKAAGCLPVESA 51

Query: 80  KDFTTEVDSQLDFIVTMVPEGKHVKSVVSELVGHYKSTGNYDPSIKTTFLDSSTIDIPTS 139
                  ++    ++TM+P GKHV+ V  + V     TG          +D STID+ T+
Sbjct: 52  AAAAEGAEA----VITMLPAGKHVEQVYEDSVFGAADTG-------AILIDCSTIDVATA 100

Query: 140 RDVHQLVKSSIPEFDFIDTPVSGGVAGARKGTLSFMLSRETHDDIDPSLTALLSKMGINI 199
           R V    ++       +D PVSGG+A A  GTL+FM+  +            L+ MG  +
Sbjct: 101 RRVADAAQAK--GLAAVDAPVSGGIAAAAGGTLTFMVGGDAA--AFERAEVFLAAMGKAV 156

Query: 200 FPCGATHGTGLAAKLANNYLLAITNIAAADSFQLAESFGLNLQNYAKLVAVSTGKSWASV 259
              G  +G G A+K+ NN LL  T +A  ++  LA+  GL+ Q +  + +VS+G  W+  
Sbjct: 157 IHAGG-NGAGQASKICNNMLLGATMVATCEALLLAQKLGLDPQTFYDIASVSSGACWSLN 215

Query: 260 DNCPIPGVYPDNNLPSDVNYEGGFITKLTRKDVVLATESAKFNNRFLMLGDIGRHWYDKA 319
              P+PG+ P    P+D  Y+GGF   L  KD+ LA E+A+  +    +G      Y K 
Sbjct: 216 TYAPLPGMGPQT--PADNGYQGGFAAGLMLKDLKLAMEAAESTHSETPMGARAAELYTKF 273

Query: 320 CEREDIANRDLSVLFEWLGDLK 341
            +  + A  D S + + LGD K
Sbjct: 274 ADAGN-AGVDFSGIIKMLGDGK 294


Lambda     K      H
   0.317    0.134    0.392 

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: 228
Number of extensions: 10
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 354
Length of database: 295
Length adjustment: 28
Effective length of query: 326
Effective length of database: 267
Effective search space:    87042
Effective search space used:    87042
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 (21.6 bits)
S2: 48 (23.1 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