GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysJ in Dyella japonica UNC79MFTsu3.2

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate N515DRAFT_3307 N515DRAFT_3307 glutamate-1-semialdehyde 2,1-aminomutase

Query= curated2:Q5SHH5
         (395 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3307 N515DRAFT_3307
           glutamate-1-semialdehyde 2,1-aminomutase
          Length = 426

 Score =  147 bits (371), Expect = 6e-40
 Identities = 104/306 (33%), Positives = 152/306 (49%), Gaps = 19/306 (6%)

Query: 33  RGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMRGEF 92
           R  GA +WD EG  YID VG +G   +GH +P V EAV+R  +  ++     P P     
Sbjct: 37  RADGAYLWDVEGKRYIDYVGSWGPMIVGHNHPRVREAVERAVKDGLSF--GTPCPAEITM 94

Query: 93  YRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSGR------TMG 146
             T+T ++ P ++ V  VNSGTEA  +A++ AR  TGR K V     + G         G
Sbjct: 95  AETITRLV-PSVDMVRMVNSGTEATMSAIRLARGATGRSKIVKFEGCYHGHGDSFLVKAG 153

Query: 147 SLSVTWEPKYREPFLP--LVEPVEFIPYNDV---EALKRAVDEETAAVILEPVQGEGGVR 201
           S ++T+      P +P    +    + YND+   EAL      + A +I+EPV G     
Sbjct: 154 SGALTFGVP-TSPGVPKAAADLTLTLAYNDLAAAEALFAEHGADIAGLIIEPVAGNMNCI 212

Query: 202 PATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVP 261
           P    +L+  R +    GALLI DE+ TG  R     A  H+GI PD+ T  K +GGG+P
Sbjct: 213 PPKDGYLQGLRALCTRHGALLIFDEVMTGF-RVALGGAQAHYGITPDLSTFGKIIGGGMP 271

Query: 262 LGAAVMREEVARSMPKGG---HGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFM 318
           +GA   R E+   +   G      T  GNP+AMAAG+A +  ++    ++R A       
Sbjct: 272 VGAYGGRRELMEQIAPAGPIYQAGTLSGNPVAMAAGLAMLELIQEAGFYDRLAARTRLLA 331

Query: 319 EKLRAI 324
           + L+A+
Sbjct: 332 DGLQAV 337


Lambda     K      H
   0.319    0.137    0.402 

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: 381
Number of extensions: 22
Number of successful extensions: 5
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: 395
Length of database: 426
Length adjustment: 31
Effective length of query: 364
Effective length of database: 395
Effective search space:   143780
Effective search space used:   143780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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