GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_3307
          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:

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