GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Acidovorax sp. GW101-3H11

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4179
          Length = 459

 Score =  189 bits (481), Expect = 1e-52
 Identities = 126/350 (36%), Positives = 176/350 (50%), Gaps = 32/350 (9%)

Query: 22  GVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLM-AM 80
           GV   HDL I + + A +WD EG  +ID  GG  V N GH +  V+ AVK Q +      
Sbjct: 48  GVGQAHDLFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGVIAAVKAQLDLYTHTC 107

Query: 81  PQTLPTPMRGEFYRTLTAILPPEL-NRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRG 139
            Q +      E    L  + P     +   + +G EA E A+K ARA+T R   +A   G
Sbjct: 108 FQVVAYEPYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIARAYTKRPGVIAFTGG 167

Query: 140 FSGRTMGSLSVTWE-PKYREPFLPL---------------------VEPVEFIPYNDVEA 177
           + GRT  +L +T +   Y+  F P                      +  VE I  ND+E 
Sbjct: 168 YHGRTNLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSVEQALHSVELIFKNDIEP 227

Query: 178 LKRAVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKR 237
                 E  AA I+EPVQGEGG   A PEF+   + +    G LLI DE+QTG GRTG  
Sbjct: 228 ------ERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQTGAGRTGTW 281

Query: 238 FAFEHFGIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAA 297
           FA E + + PD++T AK+L GG PL   V R +V  +   GG G T+ G+P+A AA +A 
Sbjct: 282 FASEQWPVAPDLITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSPVACAASLAV 341

Query: 298 IRYLERTRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVGLELKE 345
           I    + +L  R+ ++G   +  L+ + +  P I +VRG+G MV +EL E
Sbjct: 342 IEAFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFE 391


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: 413
Number of extensions: 19
Number of successful extensions: 4
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: 459
Length adjustment: 32
Effective length of query: 363
Effective length of database: 427
Effective search space:   155001
Effective search space used:   155001
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: 51 (24.3 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