GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Geobacter daltonii FRC-32

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_012645265.1 GEOB_RS00800 enoyl-CoA hydratase/isomerase family protein

Query= BRENDA::F4JML5
         (301 letters)



>NCBI__GCF_000022265.1:WP_012645265.1
          Length = 260

 Score =  150 bits (380), Expect = 2e-41
 Identities = 96/257 (37%), Positives = 135/257 (52%), Gaps = 6/257 (2%)

Query: 41  EFVKLNRLSGSDSGIIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVP 100
           EF+ L +    D  ++ ++L+RP T N +N    + L  AF    Q     VV+I S + 
Sbjct: 4   EFITLKK----DDRVLTISLNRPPT-NPLNGVFGQELFKAFSEAEQMEDITVVIITSALE 58

Query: 101 GVFCAGADLKERRTMSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMALAC 160
             F AGAD+KE      +E   +   L+   + +  +    IAAI G ALGGG E+ALAC
Sbjct: 59  KAFIAGADIKEMAAQDAAEAEQFSKLLQGANNILNRMKKIVIAAINGHALGGGCELALAC 118

Query: 161 DLRICGEN-AVFGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGL 219
           D R+     A+ GLPE GL IIPGAGGTQRL RLVG S + +++  GR +   EA   GL
Sbjct: 119 DYRLMTSGKALIGLPEAGLGIIPGAGGTQRLPRLVGLSKALDILLRGRTMSPQEALAIGL 178

Query: 220 VNICVTAGEAHEKAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLN 279
           V+  +       + ++ AQ++      A+   K A+ EGI+  +   L VE     +   
Sbjct: 179 VDKLIEPENFQAEVMQFAQELAAGAGKALGYIKAAVYEGIDFPLEQALAVERKYSAENSK 238

Query: 280 TQDRLEGLAAFAEKRKP 296
           T D  EGL AF EKR+P
Sbjct: 239 THDAKEGLTAFVEKRRP 255


Lambda     K      H
   0.318    0.134    0.373 

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: 163
Number of extensions: 9
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: 301
Length of database: 260
Length adjustment: 26
Effective length of query: 275
Effective length of database: 234
Effective search space:    64350
Effective search space used:    64350
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 24 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