GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Sphingomonas koreensis DSMZ 15582

Align crotonase (EC 4.2.1.150) (characterized)
to candidate Ga0059261_2668 Ga0059261_2668 Enoyl-CoA hydratase/carnithine racemase

Query= metacyc::MONOMER-13469
         (259 letters)



>FitnessBrowser__Korea:Ga0059261_2668
          Length = 256

 Score =  161 bits (408), Expect = 1e-44
 Identities = 100/249 (40%), Positives = 139/249 (55%), Gaps = 6/249 (2%)

Query: 13  NVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFVAGADIAEMK 71
           +VA+ITLNRP  LNAL       + A+++     D V  V+ITG+G KAF AG+DI  + 
Sbjct: 12  HVATITLNRPAKLNALTPEMAAALIASVSACNSSDAVRCVVITGAGEKAFSAGSDITTLD 71

Query: 72  DL-TAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKAKFG 130
              T  + R      +     L    KPV+AAING+ALGGG E +++ DIRIAS+ A+F 
Sbjct: 72  GYATPWDFRN----RDDYCDALRACRKPVVAAINGYALGGGLETAMAADIRIASTNARFA 127

Query: 131 QPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKLLEE 190
            PE+ LG   G G    L  ++G   A  +++TG +I+AE+AL  GLV++VV PD LL  
Sbjct: 128 APEIKLGWIGGGGMAAGLTYSMGASNAALMLFTGDMIDAEKALAWGLVSEVVAPDALLAR 187

Query: 191 AKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDRVEGMTAFVE 250
           A+ +   I   APIA    K  +        D  + YE ++   CFAT+D  EG  AF E
Sbjct: 188 AQEIARTIASRAPIAAETAKLNLRAAHTMPWDKAIEYERDLQAICFATDDAKEGRAAFAE 247

Query: 251 KRDKAFKNK 259
           KR   F+ +
Sbjct: 248 KRAPVFRRR 256


Lambda     K      H
   0.318    0.136    0.376 

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: 154
Number of extensions: 5
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: 259
Length of database: 256
Length adjustment: 24
Effective length of query: 235
Effective length of database: 232
Effective search space:    54520
Effective search space used:    54520
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