GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Klebsiella michiganensis M5al

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__Koxy:BWI76_RS11670
          Length = 406

 Score =  264 bits (674), Expect = 4e-75
 Identities = 154/385 (40%), Positives = 218/385 (56%), Gaps = 39/385 (10%)

Query: 23  VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82
           VY     + VRG+G+R+WD +G EYID  GG  V  LGH +P +V+A+  QA        
Sbjct: 17  VYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQA-------- 68

Query: 83  TLPTPMRGEFYRTLTAI-------LPPEL------NRVFPVNSGTEANEAALKFARAHT- 128
                  G+F+ T           L  +L      +RVF  NSG EANEAALK AR +  
Sbjct: 69  -------GKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAH 121

Query: 129 ---GRKK--FVAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVD 183
              G +K   VA    F GRT+ ++S   +P Y + F PL   ++   YND+++ K  +D
Sbjct: 122 DRFGSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALID 181

Query: 184 EETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHF 243
           + T AVI+EP+QGEGGV PA  +FLR  RE+     ALLI DE+QTG+GRTG+ +A+ H+
Sbjct: 182 DNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHY 241

Query: 244 GIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLER 303
           G+ PD+L+ AKALGGG P+GA +  E  A  M  G HGTT+GGNPLA A        +  
Sbjct: 242 GVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINT 301

Query: 304 TRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKEK---AAPYIARLEKEH 358
             +     +   WF E+L AI +     +E+RG+GL++G  LK++    A  I+    E 
Sbjct: 302 REVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEE 361

Query: 359 RVLALQAGPTVIRFLPPLVIEKEDL 383
            ++ L AG  V+RF P L+I ++++
Sbjct: 362 GLMILIAGANVVRFAPALIISEDEV 386


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: 379
Number of extensions: 16
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: 406
Length adjustment: 31
Effective length of query: 364
Effective length of database: 375
Effective search space:   136500
Effective search space used:   136500
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