GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Shewanella oneidensis MR-1

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate 200845 SO1680 enoyl-CoA hydratase/isomerase family protein (NCBI ptt file)

Query= BRENDA::Q1D5Y4
         (258 letters)



>FitnessBrowser__MR1:200845
          Length = 257

 Score =  153 bits (386), Expect = 4e-42
 Identities = 88/235 (37%), Positives = 127/235 (54%)

Query: 24  NAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERATMAEDEVRAFLDG 83
           N  +   L+ L   V  +++++D+ A+V+TG G+K F AGADLK  +   +    +    
Sbjct: 23  NTWTAQSLQALKAKVLELNANKDIYALVLTGEGNKFFSAGADLKLFSDGDKGNAASMAKH 82

Query: 84  LRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLTEVKLGIIPGGGG 143
               F  + +   V IAAING A+GGG E+ALACD+R+A   A + L E  +G++P  GG
Sbjct: 83  FGEAFETLSQFRGVSIAAINGYAMGGGLEVALACDIRIAETQAVMALPEATVGLLPCAGG 142

Query: 144 TQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAVAYGLAESVVENAPI 203
           TQ L  LVG G AK +IL   R+NAA+A ++ L   +   G  L  A  LA  V   +P 
Sbjct: 143 TQNLTALVGEGWAKRMILCGERVNAAQALNLRLVEEVVETGEALNAAIALAAKVANQSPS 202

Query: 204 AVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLRAFAEKRAPVYKGR 258
           +V   K  I  G  +    AL +E   +  +  TED+ EG+ AF EKR   +K R
Sbjct: 203 SVTACKTLIQAGRQMPRSQALPIEHELFVGLFDTEDQAEGVNAFLEKRKADWKNR 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: 112
Number of extensions: 3
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: 257
Length adjustment: 24
Effective length of query: 234
Effective length of database: 233
Effective search space:    54522
Effective search space used:    54522
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