GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas fluorescens GW456-L13

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate PfGW456L13_4910 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910
          Length = 413

 Score =  261 bits (668), Expect = 2e-74
 Identities = 154/402 (38%), Positives = 221/402 (54%), Gaps = 15/402 (3%)

Query: 6   LEDWRALLEAEKTLDSGVYNKHDLLIV---RGQGARVWDAEGNEYIDCVGGYGVANLGHG 62
           L+  R LLE +    + + + +  L +   +G G R+WD  G EY+D V G  V N+GH 
Sbjct: 11  LQKHRPLLELDVMTAACLMSTYQPLALSFNKGLGTRLWDQAGREYLDAVAGVAVTNVGHS 70

Query: 63  NPEVVEAVKRQAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALK 122
           +P++V A+  QA  L+          +    + LT +    ++R F  NSG EANE ALK
Sbjct: 71  HPKIVAAITEQAGLLLHTSNLYSIDWQQRLAQKLTQLAG--MDRAFFNNSGAEANETALK 128

Query: 123 FARAHTGRKKF-----VAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEA 177
            AR H   K       V     F GRT+G+LS +  P  R  F  L      +P+ D+ A
Sbjct: 129 IARLHGWHKGIEQPLVVVMENAFHGRTLGTLSASDGPAVRLGFNKLPGDFVKVPFGDLGA 188

Query: 178 L---KRAVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRT 234
           L   ++A      AV++EP+QGE GV+ A P +L A RE+   +  LL+LDEIQTG+GRT
Sbjct: 189 LDKVQQAFGSRIVAVLMEPIQGESGVQLAPPGYLSAVRELCNRRSWLLMLDEIQTGIGRT 248

Query: 235 GKRFAFEHFGIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAG 294
           G+ FAF+H GIVPD++TLAK LG GVP+GA + R + A     G HG+TFGGNPLA   G
Sbjct: 249 GQWFAFQHEGIVPDVMTLAKGLGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVG 308

Query: 295 VAAIRYLERTRLWERAAELGPWFMEKLRA--IPSPKIREVRGMGLMVGLELKEKAAPYIA 352
              +  +E   L E A   G   +E+LR     +P + ++RG GLM+G+ELK+       
Sbjct: 309 CTVLDIVEEQGLLENARLQGARLLERLRTELAGNPNVSQIRGQGLMIGIELKQPIRDLSL 368

Query: 353 RLEKEHRVLALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVL 394
              ++H +L        IR LPPL +++ ++E +V  V  V+
Sbjct: 369 IAARDHGLLINVTRGNTIRLLPPLTLDEREVEMIVRGVGRVV 410


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: 417
Number of extensions: 21
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: 413
Length adjustment: 31
Effective length of query: 364
Effective length of database: 382
Effective search space:   139048
Effective search space used:   139048
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