GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas litoralis 2SM5

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_090275068.1 BLU11_RS15910 3-hydroxyacyl-CoA dehydrogenase

Query= reanno::psRCH2:GFF2389
         (257 letters)



>NCBI__GCF_900105005.1:WP_090275068.1
          Length = 697

 Score =  123 bits (309), Expect = 9e-33
 Identities = 83/200 (41%), Positives = 108/200 (54%), Gaps = 7/200 (3%)

Query: 4   ETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAA 63
           + + ++ Q  VA+I +N P  +NAL   +   L  +    EAD Q+  IVL      F A
Sbjct: 3   DVVTLERQGAVAVIRVNNPP-VNALGVAVREGLQNSFNAAEADAQVKAIVLVCEGNTFIA 61

Query: 64  GADIKEMAELTYPQI-YLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIFAA 122
           GADIKE  +   PQ   L D  +    I    KP IA + G ALGGG E+AL C    A 
Sbjct: 62  GADIKEFGKP--PQAPSLPDVISG---IEAGSKPSIAVIHGTALGGGLEVALSCHYRIAR 116

Query: 123 DNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPA 182
            +A+ G PEV LG+LPG GGTQRL R VG AKA+DM ++G  + A EA   G+V  +F  
Sbjct: 117 KDAKVGLPEVKLGLLPGAGGTQRLPRVVGVAKALDMIVSGTPIGAVEANELGVVDELFDG 176

Query: 183 ESLLEETLKAARVIAEKSLP 202
           E L      A ++IAE   P
Sbjct: 177 ELLAAGLTFAEKLIAEGQGP 196


Lambda     K      H
   0.321    0.135    0.375 

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: 377
Number of extensions: 13
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: 257
Length of database: 697
Length adjustment: 32
Effective length of query: 225
Effective length of database: 665
Effective search space:   149625
Effective search space used:   149625
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 (21.9 bits)
S2: 50 (23.9 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