GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas simiae WCS417

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate GFF1577 PS417_08025 acetylornithine aminotransferase

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__WCS417:GFF1577
          Length = 389

 Score =  262 bits (670), Expect = 1e-74
 Identities = 151/382 (39%), Positives = 212/382 (55%), Gaps = 12/382 (3%)

Query: 24  YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83
           Y    L   RG G R+WD +G EY+D V G  V N+GH +P +V A+  QA  L+     
Sbjct: 10  YQPLALSFTRGLGTRLWDQQGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLHTSNL 69

Query: 84  LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAM-----R 138
                +    + LT +    L+R F  NSG EANE ALK AR H  +K   A +      
Sbjct: 70  YSIDWQQRLAQRLTQL--SGLDRAFFNNSGAEANETALKLARLHGWKKGIEAPLVVVMEN 127

Query: 139 GFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDV---EALKRAVDEETAAVILEPVQ 195
            F GRT+G+L+ +  P  R  F  L      + + D+   EA+ +A      AV+LEP+Q
Sbjct: 128 AFHGRTLGTLAASDGPSVRLGFQQLPGDFLKVRFGDLAALEAITKAFGPRITAVLLEPIQ 187

Query: 196 GEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKA 255
           GE GV PA   +L+A R+    +G L++LDEIQTG+GRTG  FAF+H GIVPD++TLAK 
Sbjct: 188 GESGVLPAPSGYLQALRDHCTRQGWLMMLDEIQTGIGRTGTWFAFQHEGIVPDVMTLAKG 247

Query: 256 LGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGP 315
           LG GVP+GA + R  VA+    G HG+TFGGNPLA   G   +  +E   L + AA+ G 
Sbjct: 248 LGNGVPIGACLARAAVAQLFTPGSHGSTFGGNPLACRVGCTVLDIIEEQGLLQNAAQQGE 307

Query: 316 WFMEKLRA--IPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVIRFL 373
             + +LR       ++  +RG GLM+G+EL         R  +EH +L       +IR L
Sbjct: 308 RLLARLRVELNEHAQVVAIRGQGLMIGIELASPCRDLAQRAAQEHGLLINVTRGKIIRLL 367

Query: 374 PPLVIEKEDLERVVEAVRAVLA 395
           PPL ++ +++E +V A+  +LA
Sbjct: 368 PPLTLDTQEVEMIVRAITRLLA 389


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: 356
Number of extensions: 26
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: 389
Length adjustment: 31
Effective length of query: 364
Effective length of database: 358
Effective search space:   130312
Effective search space used:   130312
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