GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Shewanella oneidensis MR-1

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 199805 SO0617 acetylornithine aminotransferase (NCBI ptt file)

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__MR1:199805
          Length = 405

 Score =  249 bits (635), Expect = 1e-70
 Identities = 152/380 (40%), Positives = 213/380 (56%), Gaps = 22/380 (5%)

Query: 32  VRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMRGE 91
           VRG+G+RVWD EGNE+ID  GG  V  LGH +P +V A+K Q E L  +   +      E
Sbjct: 28  VRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNALKTQGEKLWHLSNVMTNEPALE 87

Query: 92  FYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRK------KFVAAMRGFSGRTM 145
               L      E  RV+  NSG EANEAALK AR +   K      + +A  + F GRT 
Sbjct: 88  LATKLVNSTFAE--RVYFANSGAEANEAALKLARRYALEKHGVEKDEIIAFDKAFHGRTF 145

Query: 146 GSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGEGGVRPATP 205
            ++SV  +  Y + F P  + +  +P+NDV AL+ AV ++T A++LEP+QGEGG+  A P
Sbjct: 146 FTVSVGGQAAYSDGFGPKPQSITHLPFNDVAALEAAVSDKTCAIMLEPLQGEGGIIDADP 205

Query: 206 EFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGAA 265
            FL+A RE+  +  AL+I DE+QTG+GRTG+ +A+    IVPDILT AKALGGG P+ A 
Sbjct: 206 AFLKAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTDIVPDILTTAKALGGGFPIAAM 265

Query: 266 VMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIP 325
           +   E+A  +  G HG+T+GGNPLA A G A +  +    +            + L  I 
Sbjct: 266 LTTTEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTPEVLNGVKHREQLLRDGLNKIN 325

Query: 326 SP--KIREVRGMGLMVGLELKE----KAAPYIARLEKEHRVLALQAGPTVIRFLPPLVIE 379
                  EVRG GL++G  L E    ++  ++     E  +++L AG  V+RF P LVI 
Sbjct: 326 EKYHVFSEVRGKGLLLGAVLNEQYQGRSRDFLVASVAE-GLMSLMAGANVVRFAPSLVIP 384

Query: 380 KEDL-------ERVVEAVRA 392
           + D+       ER V ++ A
Sbjct: 385 EADIAEGLARFERAVASIAA 404


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: 394
Number of extensions: 20
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: 405
Length adjustment: 31
Effective length of query: 364
Effective length of database: 374
Effective search space:   136136
Effective search space used:   136136
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