GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysU in Pseudomonas putida KT2440

Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate PP_1986 PP_1986 3-isopropylmalate dehydratase small subunit

Query= SwissProt::Q58667
         (170 letters)



>FitnessBrowser__Putida:PP_1986
          Length = 214

 Score = 66.6 bits (161), Expect = 3e-16
 Identities = 44/122 (36%), Positives = 64/122 (52%), Gaps = 24/122 (19%)

Query: 13  DVDTDAIIP------------GP-------YLRTTDPYELASHCMAGIDENFP---KKVK 50
           +VDTD IIP            GP       YL    PY+   +    ++E F     + +
Sbjct: 18  NVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPYQ--DNSKRPLNEEFVLNHARYQ 75

Query: 51  EGDVIVAGENFGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANTDEI 110
              V++A ENFGCGSSRE A  A+   G +++IA SFA IF+ N+   GL+PII + +E+
Sbjct: 76  GASVLLARENFGCGSSREHAPWALDEYGFRSIIAPSFADIFFNNSFKNGLLPIILSDEEV 135

Query: 111 KD 112
            +
Sbjct: 136 DE 137


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: 109
Number of extensions: 5
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: 170
Length of database: 214
Length adjustment: 20
Effective length of query: 150
Effective length of database: 194
Effective search space:    29100
Effective search space used:    29100
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: 44 (21.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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