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_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3308
          Length = 411

 Score =  271 bits (692), Expect = 3e-77
 Identities = 173/405 (42%), Positives = 226/405 (55%), Gaps = 28/405 (6%)

Query: 11  ALLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAV 70
           +L++  K     VY   ++++  G+GARVWD EG +Y+D   G  V  LGH +P++V+A+
Sbjct: 9   SLIDLGKRYWLPVYRPREVVLDHGKGARVWDTEGRDYVDLGAGIAVNALGHQDPDLVDAL 68

Query: 71  KRQAETLMAMPQTLPTPMRGEFYRTLTAILPPEL-------NRVFPVNSGTEANEAALKF 123
             QA  L              FY      L  EL        RVF  NSGTEANEAA+K 
Sbjct: 69  VTQARKLWHSSNV--------FYTEPPLHLAEELVQASGFAERVFLCNSGTEANEAAIKL 120

Query: 124 AR---AHTGR---KKFVAAMRG-FSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVE 176
            R   A  GR   ++ +   RG F GRT+ +++ T +PKY+E + PL     ++ +NDV 
Sbjct: 121 VRKWAASKGRAPEQRVILTFRGSFHGRTLAAVTATAQPKYQENYEPLPGGFRYLDFNDVA 180

Query: 177 ALKRAVDE-ETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTG 235
            L+ A  + + AAV+LEPVQGEGGV PA+P F+R ARE+     ALL+LDEIQ GMGRTG
Sbjct: 181 GLEAAFAQGDVAAVMLEPVQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTG 240

Query: 236 KRFAFEHFGIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGV 295
             FA    G+ PDI+TLAKALG G P+GA +   +VA  M  G HGTTFGGNP+A A   
Sbjct: 241 TLFAHAQDGVTPDIVTLAKALGCGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVAR 300

Query: 296 AAIRYLERTRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKEK---AAPY 350
            A+R L    L    A+      + L AI        EVRG GLM+G  L E     A  
Sbjct: 301 VALRKLASAELMANVAKQAQALRDGLAAIDGELKLFAEVRGRGLMLGAVLAEAYKGRAGE 360

Query: 351 IARLEKEHRVLALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVLA 395
           +      H +L LQAGP V+RF+PPL I   DL   +  +RA LA
Sbjct: 361 VLDHAAAHGLLVLQAGPDVLRFVPPLNITDADLAEGLARLRAALA 405


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: 414
Number of extensions: 23
Number of successful extensions: 6
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: 411
Length adjustment: 31
Effective length of query: 364
Effective length of database: 380
Effective search space:   138320
Effective search space used:   138320
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