GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysY in Pseudomonas putida KT2440

Align Putative [LysW]-L-2-aminoadipate 6-phosphate reductase; EC 1.2.1.103 (uncharacterized)
to candidate PP_0432 PP_0432 N-acetyl-gamma-glutamyl-phosphate reductase 1

Query= curated2:B9KZP8
         (352 letters)



>FitnessBrowser__Putida:PP_0432
          Length = 344

 Score =  236 bits (603), Expect = 5e-67
 Identities = 150/354 (42%), Positives = 194/354 (54%), Gaps = 14/354 (3%)

Query: 2   VVSVAILGGSGYTGGELLRLLLSHPEVEVKQVTSRSRAGKFVHTVHPNLRKR-TALKFVP 60
           ++ V I+GG+GYTG ELLRLL  HP+ EV  +TSRS AG  V  ++PNLR     L F  
Sbjct: 1   MIKVGIVGGTGYTGVELLRLLAQHPQAEVAVITSRSEAGVAVADMYPNLRGHYDGLAFSV 60

Query: 61  PE--ALEPVDLLFACLPHGETAPIVDRLLELAPIVIDLSADFRLRDPAAYEQWYHWTHPR 118
           P+  AL   D++F   PHG    +   LL     VIDLSADFRL+D   + +WY   H  
Sbjct: 61  PDSKALGACDVVFFATPHGVAHALAGELLAAGTKVIDLSADFRLQDATEWGKWYGQPHGA 120

Query: 119 PDLLAQAVYGLPELHREEIRNARYIACPGCNSTTVILGLAPLFRAGLIDLDLPVTVECKV 178
           P+LL  AVYGLPE++RE+IR AR IA PGC  T   LG  PL  AGL D    +  +CK 
Sbjct: 121 PELLKDAVYGLPEVNREKIRQARLIAVPGCYPTATQLGFLPLLEAGLAD-PSRLIADCKS 179

Query: 179 GSSGAGGEAGPASHHPERSGVIRPFKPGGHRHTAEVLQELTV-CGRTPSLGLSVTSVEAV 237
           G SGAG  A   S   E    ++ +   GHRH  E+ Q L +  G+   L         +
Sbjct: 180 GVSGAGRGAAVGSLFCEAGESMKAYAVKGHRHLPEISQGLRLAAGKDIGLTFVPHLTPMI 239

Query: 238 RGILATAHLFPKQPLTDRDLWQVYRAAYGQEPFIRLVKEASGIHRYPEPKILAGSNYCDI 297
           RGI AT  L+     T  DL  ++   Y  EPF+ ++   S    +PE + + G+N C I
Sbjct: 240 RGIHAT--LYANVVDTSVDLQALFEKRYADEPFVDVMPAGS----HPETRSVRGANVCRI 293

Query: 298 GWELDELPGGRQRLVVMSAIDNLMKGAAGQAVQAMNIRLGFPETLGLEFPGLHP 351
                  P G   +VV+S IDNL+KGA+GQAVQ +NI  G  E +GL   GL P
Sbjct: 294 A---VHRPQGGDLVVVLSVIDNLVKGASGQAVQNLNILFGLDERMGLSHAGLLP 344


Lambda     K      H
   0.321    0.140    0.431 

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: 387
Number of extensions: 18
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: 352
Length of database: 344
Length adjustment: 29
Effective length of query: 323
Effective length of database: 315
Effective search space:   101745
Effective search space used:   101745
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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