GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Shewanella loihica PV-4

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 5208561 Shew_1072 chorismate mutase (RefSeq)

Query= BRENDA::Q9YEJ7
         (270 letters)



>FitnessBrowser__PV4:5208561
          Length = 654

 Score =  100 bits (250), Expect = 6e-26
 Identities = 78/244 (31%), Positives = 118/244 (48%), Gaps = 9/244 (3%)

Query: 13  SEERRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRT 72
           +E  + T V    ++IG G    IA     +  +   + A  +KEAG   +         
Sbjct: 419 AEHPQVTSVICRQLQIGNGQFGAIAQLALSQESDHYGQLAKQIKEAGFQAVT-------V 471

Query: 73  SPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLL 132
           S  +   +    L  +RRA ++  L  +  +     +   S +ADML I  + M N  LL
Sbjct: 472 SELNTNPMANRQLSEMRRALNQFDLACIVAIEHESELTLASDHADMLLISGKQMHNRDLL 531

Query: 133 REVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAA 192
            +VG    PV+L+R    +++E L AAE IL  GN Q+VL E GIRTF    R TLD++ 
Sbjct: 532 EQVGALHMPVILERNTMASLDEWLGAAEVILAAGNQQLVLSEAGIRTFNEQQRPTLDLSG 591

Query: 193 VAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEV-HPNPEEALSDAKQQ 251
           +  LKE +HLPV+++  +   +  L  + A A  A  ADGL++ V  P   +  SD   +
Sbjct: 592 LISLKERSHLPVLLNTRYACQQEELA-SQAGAAKALKADGLVLGVSDPQQLKGHSDILAR 650

Query: 252 LTPG 255
           L  G
Sbjct: 651 LYRG 654


Lambda     K      H
   0.318    0.136    0.392 

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: 285
Number of extensions: 5
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: 270
Length of database: 654
Length adjustment: 31
Effective length of query: 239
Effective length of database: 623
Effective search space:   148897
Effective search space used:   148897
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.

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