GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Phaeobacter inhibens BS107

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate GFF3794 PGA1_262p01980 putative enoyl-CoA hydratase

Query= BRENDA::Q1D5Y4
         (258 letters)



>FitnessBrowser__Phaeo:GFF3794
          Length = 263

 Score =  146 bits (369), Expect = 4e-40
 Identities = 84/255 (32%), Positives = 134/255 (52%), Gaps = 4/255 (1%)

Query: 7   DARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADL 66
           +  G + + T++   + NA++ A    L  L+  +     +RA+++TGAG++AF AG D+
Sbjct: 8   ERNGAVAVLTLNRPEKLNALNYATNDCLLSLLNAIEIDPSIRAIILTGAGERAFSAGGDI 67

Query: 67  KERATMA----EDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVA 122
            E         ++ VR F    +     +E      IAA+NG A GGG E+  A  L VA
Sbjct: 68  HEFTESVKAGVDEAVRDFCKRGQTMTARLEAFQKPIIAAVNGIAFGGGCEITEAVHLAVA 127

Query: 123 APAAELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAP 182
           +  A     E+ +GI P  GGTQRL RL G  RA +L+LT    +A  A  +GL NR+ P
Sbjct: 128 SERAMFAKPEINIGIPPTFGGTQRLPRLAGRKRALELLLTGDTFSAQRACEMGLVNRIVP 187

Query: 183 EGHLLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLE 242
              L+  A+ LA+ ++ ++P+A +    A+  G    +D+ L +E  ++  +  T+D  E
Sbjct: 188 HDELMPAAFDLADRIIRHSPLAASRIITAVTRGINTTIDEGLLIEREQFARMAATKDVHE 247

Query: 243 GLRAFAEKRAPVYKG 257
           GL A+  +R P Y G
Sbjct: 248 GLGAWIARRTPEYVG 262


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: 151
Number of extensions: 4
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: 258
Length of database: 263
Length adjustment: 25
Effective length of query: 233
Effective length of database: 238
Effective search space:    55454
Effective search space used:    55454
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 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