GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroL in Dyella japonica UNC79MFTsu3.2

Align Shikimate kinase 1; SK 1; Shikimate kinase I; SKI; EC 2.7.1.71 (characterized)
to candidate N515DRAFT_1793 N515DRAFT_1793 shikimate kinase

Query= SwissProt::P0A6D7
         (173 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1793
          Length = 179

 Score =  145 bits (365), Expect = 5e-40
 Identities = 73/168 (43%), Positives = 111/168 (66%), Gaps = 1/168 (0%)

Query: 6   NIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQEIEKRTGADVGWVFDLEGEEGFRDREEK 65
           N+F+VGP GAGK++IGR+LA    +EF D DQEIE+  GA V  VF+LEGE GFR RE  
Sbjct: 6   NLFIVGPTGAGKTSIGRRLAAHYELEFLDLDQEIERHCGATVSTVFELEGEAGFRRREST 65

Query: 66  VINELTEKQGIVLATGGGSVKSRETRNRLSARGVVVYLETTIEKQLARTQRDKKRPLLHV 125
           +++  T + G++LATG G+V   + R  L+ RG V++L+ T+E+QL R  RD+ RPLL  
Sbjct: 66  LLDACTARSGVLLATGAGAVLDPDNRRLLAGRGYVLWLQATLEQQLERLARDRSRPLLAG 125

Query: 126 ETPPREVLEALANERNPLYEEIADVTIRTDDQSAKVVANQIIHMLESN 173
           E    + L+A+A  R PLY ++AD+ I  + +  +  + + I +++ +
Sbjct: 126 EDRSAK-LQAMAGIRTPLYADVADLVIPGEHELVQAASERSIALIDQH 172


Lambda     K      H
   0.313    0.132    0.359 

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: 98
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: 173
Length of database: 179
Length adjustment: 19
Effective length of query: 154
Effective length of database: 160
Effective search space:    24640
Effective search space used:    24640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 44 (21.6 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