GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysU in Phaeobacter inhibens BS107

Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate GFF1856 PGA1_c18830 aconitate hydratase AcnA

Query= SwissProt::Q58667
         (170 letters)



>FitnessBrowser__Phaeo:GFF1856
          Length = 895

 Score = 57.0 bits (136), Expect = 8e-13
 Identities = 47/155 (30%), Positives = 67/155 (43%), Gaps = 31/155 (20%)

Query: 22  GPYLRTTDPYELASHCMAGIDENFPKKVKEGDVIVAGENFGCGSSREQAVIAIKYCGIKA 81
           GP    T  YE +   MA  ++  P       V+  GE +G GSSR+ A       G+KA
Sbjct: 745 GPDGEQTSVYEAS---MAYQEQGIPL------VVFGGEQYGAGSSRDWAAKGTALLGVKA 795

Query: 82  VIAKSFARIFYRNAINVGLIPI--------------------IANTDEIKDGDIVEIDLD 121
           VIA+SF RI   N + +G+IP                     I   D IK  + V  D+ 
Sbjct: 796 VIAESFERIHRSNLVGMGVIPFEFTGGDTRKSLNLTGDETVSIHGLDTIKPQEEVSCDIT 855

Query: 122 KEEIVITNKNKTIKCETPKGLEREILAAGGLVNYL 156
             +   T K  T+KC      E E +  GG+++Y+
Sbjct: 856 YGD--GTTKTITLKCRIDTAPEIEYIEHGGVLHYV 888


Lambda     K      H
   0.318    0.139    0.399 

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: 367
Number of extensions: 28
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 170
Length of database: 895
Length adjustment: 30
Effective length of query: 140
Effective length of database: 865
Effective search space:   121100
Effective search space used:   121100
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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