GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroL in Magnetospirillum magneticum AMB-1

Align Shikimate kinase; Short=SK; EC 2.7.1.71 (characterized, see rationale)
to candidate WP_050750826.1 AMB_RS19870 shikimate kinase

Query= uniprot:AROK_CAUVN
         (200 letters)



>NCBI__GCF_000009985.1:WP_050750826.1
          Length = 191

 Score =  179 bits (453), Expect = 4e-50
 Identities = 99/174 (56%), Positives = 121/174 (69%), Gaps = 4/174 (2%)

Query: 26  LAPLRA----KTIVLVGLMGVGKSSVGRRLANVLGLPFRDADNEVEAAAGRSISEIFAEL 81
           LAPL +    +TIVLVGLMG GKS VGRRLA  LGL F D+D E EAA+G SIS+ FA  
Sbjct: 8   LAPLLSGRIGRTIVLVGLMGAGKSCVGRRLAARLGLDFVDSDAEFEAASGSSISDYFARF 67

Query: 82  GEPAFRDGERRVIARLLDEPPHVLATGGGAFVNAETRALINEKAVSVWLKADVELLARRV 141
           GE AFR+GER+VIARLLD PP VLATGGGAFV+  TR  I     SVW++AD+ELL +R 
Sbjct: 68  GEAAFREGERKVIARLLDGPPVVLATGGGAFVDPTTRERIKAAGTSVWIRADLELLLKRT 127

Query: 142 SRKDNRPLVRGKDPVKVLTELAEARYPAYAEAQVHVETGDTPHMVAVEAILTAL 195
             +D+RPL++  DP ++L  L EARYP YAEA + VE+ D      V  ++  L
Sbjct: 128 VGRDHRPLLKQGDPREILGRLMEARYPIYAEADIIVESTDEVPEATVIRVMEGL 181


Lambda     K      H
   0.316    0.132    0.369 

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: 146
Number of extensions: 4
Number of successful extensions: 1
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: 200
Length of database: 191
Length adjustment: 20
Effective length of query: 180
Effective length of database: 171
Effective search space:    30780
Effective search space used:    30780
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 (21.6 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