GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Limnohabitans curvus MWH-C5

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_108359319.1 B9Z44_RS10090 enoyl-CoA hydratase

Query= BRENDA::Q1D5Y4
         (258 letters)



>NCBI__GCF_003063475.1:WP_108359319.1
          Length = 259

 Score =  150 bits (380), Expect = 2e-41
 Identities = 91/245 (37%), Positives = 136/245 (55%), Gaps = 2/245 (0%)

Query: 12  IEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERAT 71
           + + T++   + NA++  ++ ELG+ +    ++  +  +VITG+ +KAF AGAD+   AT
Sbjct: 15  VGVITLNRPKQLNALNAGLMVELGQALKDFDANEAIGCMVITGS-EKAFAAGADIGAMAT 73

Query: 72  MAEDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLT 131
            +  +V    D + R +  I       IAA++G ALGGG ELA+ CD  +AA  A+ G  
Sbjct: 74  YSFADVYKN-DYITRDWETIRSIRKPVIAAVSGFALGGGCELAMMCDFIIAADNAKFGQP 132

Query: 132 EVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAVAY 191
           E+KLGIIPG GGTQRL R VG  +A DL LT R ++A EA   GL +R+ P   L+    
Sbjct: 133 EIKLGIIPGAGGTQRLPRAVGKSKAMDLALTGRMMDATEAERAGLVSRVVPLDKLMEETL 192

Query: 192 GLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLRAFAEKR 251
           G A  +   + IA   AK +++      L D +  E R +  +  T D+ EG+ AF  KR
Sbjct: 193 GAALMICGYSQIAAMAAKESVNRAFEGTLADGVMFERRLFHALFATADQKEGMDAFVNKR 252

Query: 252 APVYK 256
              +K
Sbjct: 253 PADFK 257


Lambda     K      H
   0.319    0.136    0.380 

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: 129
Number of extensions: 6
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: 258
Length of database: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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