GapMind for Amino acid biosynthesis

 

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

Align Shikimate kinase; SK; EC 2.7.1.71 (uncharacterized)
to candidate WP_011382615.1 AMB_RS00855 helix-turn-helix domain-containing protein

Query= curated2:A5GQN5
         (195 letters)



>NCBI__GCF_000009985.1:WP_011382615.1
          Length = 290

 Score = 80.1 bits (196), Expect = 4e-20
 Identities = 52/160 (32%), Positives = 84/160 (52%), Gaps = 5/160 (3%)

Query: 21  LVGMMGSGKSTVGPLLAKALGYRFLDADAVISQAAGCSIPEIFERDGEEGFRQLERQVLQ 80
           L+G+ G+GK+T+G  +A      F    ++I Q AG  + EI    G++G+R+LE   L+
Sbjct: 122 LIGLRGAGKTTLGEAVAGRFAAPFRRITSMIEQMAGMDMTEILLSTGQKGYRKLEYSALE 181

Query: 81  Q-LSQWHSLVVATGGGIVTVPANWGELRQG-VVIWLDVAEEELMRRLQADPGGRPLLAGD 138
             L    ++V+  GG +V+ P  +  L Q    IW+  + E+ MRR+      RP +AG 
Sbjct: 182 NTLEAQPTMVLEAGGSLVSEPRTFELLLQSCFTIWVQASPEDHMRRVMGQGDLRP-IAGQ 240

Query: 139 DPAGR--LHGLLEKRQPLYGQADLRVSAQGEGASDISERI 176
             A    L  +LE R+ LYG+AD  ++  G   +D  E +
Sbjct: 241 QMAAMEDLKAILEARRHLYGRADAVINTSGRSIADSVEEM 280


Lambda     K      H
   0.316    0.137    0.408 

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: 144
Number of extensions: 7
Number of successful extensions: 3
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: 195
Length of database: 290
Length adjustment: 23
Effective length of query: 172
Effective length of database: 267
Effective search space:    45924
Effective search space used:    45924
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: 46 (22.3 bits)

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

Links

Downloads

Related tools

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