GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Escherichia coli BW25113

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 17148 b3073 putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent (RefSeq)

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__Keio:17148
          Length = 459

 Score =  264 bits (674), Expect = 4e-75
 Identities = 158/373 (42%), Positives = 218/373 (58%), Gaps = 18/373 (4%)

Query: 41  DAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMRGEFYRTLTAIL 100
           D +G E+IDC+GG+G+ N+GH NP VV AV+ Q        Q L  P+R    +TL A+ 
Sbjct: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137

Query: 101 PPELNRVFPVNSGTEANEAALKFARAHT---GRKKFVAAMRGFSGRTMGSLSVTWEPKYR 157
           P +L   F  NSGTE+ EAALK A+A+    G+  F+A    F G+++G+LS T +  +R
Sbjct: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFR 197

Query: 158 EPFLPLVEPVEFIPYNDVEALKRAVDE------ETAAVILEPVQGEGGVRPATPEFLRAA 211
           +PF+PL+     +P+ ++EA++ A++E      + AAVILEP+QGEGGV    P +L A 
Sbjct: 198 KPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAV 257

Query: 212 REITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGV-PLGAAVMREE 270
           R++  E GAL+ILDE+QTGMGRTGK FA EH  + PDIL LAKALGGGV P+GA +  EE
Sbjct: 258 RKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEE 317

Query: 271 VARSMPKGG--HGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIP--- 325
           V   +      H TTFGGNPLA AA +A I  L    L  +A + G   ++  R +    
Sbjct: 318 VFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREY 377

Query: 326 SPKIREVRGMGLMVGLELKEKAAPYIARLEK-EHRVLALQA--GPTVIRFLPPLVIEKED 382
              ++E RG G+++ +E  +    Y    E    RVL          IR  PPL +  E 
Sbjct: 378 PDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQ 437

Query: 383 LERVVEAVRAVLA 395
            E V++A R  LA
Sbjct: 438 CELVIKAARKALA 450


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: 404
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