GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Lacinutrix algicola AKS293

Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_055434605.1 ASC41_RS00020 glutamate-1-semialdehyde 2,1-aminomutase

Query= SwissProt::H8WR05
         (434 letters)



>NCBI__GCF_001418085.1:WP_055434605.1
          Length = 426

 Score =  201 bits (510), Expect = 5e-56
 Identities = 137/416 (32%), Positives = 203/416 (48%), Gaps = 22/416 (5%)

Query: 24  SQRQFEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTAGV 80
           S   F A  + +PG  +  V  +      P+ +   +GA L+D DG+   D+I  +   +
Sbjct: 6   SSTLFAAAEKVIPGGVNSPVRAFKAVGGTPIFVKEAKGAYLYDEDGNTLIDYINSWGPMI 65

Query: 81  YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140
            GH+   + +AVIE  + G +      +E  +A L     P I+++RF NSGTEA + A+
Sbjct: 66  LGHAFEPVVNAVIEKAKKGTSFGMPTEIETEIAELAVSMVPNIDKIRFVNSGTEACMSAV 125

Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTT---VPFDFLVLPYND 186
             A  +TG+ KI+ F+G YHG           G + FG+  SP        D L+  YND
Sbjct: 126 RLARGYTGKDKIIKFAGCYHGHSDSFLIQAGSGAVTFGSPNSPGVTEGTAKDTLLANYND 185

Query: 187 AQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS- 245
                A I  +  EIA +++EP+ G  GCIP    FLQ LR        LL+FDEVMT  
Sbjct: 186 LTNVEALINANKNEIACIIIEPVAGNMGCIPPLDGFLQGLRSLCDANDVLLIFDEVMTGF 245

Query: 246 RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNNV 305
           RLA  G+    G+ +D+   GK IGGG+  GAF  R ++M    P  GP+  +GT + N 
Sbjct: 246 RLAKGGVQELYGVDADIVCFGKVIGGGLPVGAFAARNEIMNHLAP-LGPVYQAGTLSGNP 304

Query: 306 MTMAAGYAGLTKLFTP-EAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQ 364
           + MAAG A LT L    E    LAE+ E L   L  +     +      IGS+++ HF  
Sbjct: 305 LAMAAGLAMLTTLNNDVEVFNRLAEKTEYLHKGLAKVLDKNNITHTINRIGSMISVHFDA 364

Query: 365 GDVRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGFVV--LSLPLTDADIDRYVAA 418
             V   +  A  +    +  F  +LN+ +Y +P  F    ++  LT  D+D+ + A
Sbjct: 365 EPVIDFKTAANGNNETFKTFFHGMLNQGVYIAPSAFETWFITDALTYEDLDKTIEA 420


Lambda     K      H
   0.322    0.138    0.408 

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: 416
Number of extensions: 22
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: 434
Length of database: 426
Length adjustment: 32
Effective length of query: 402
Effective length of database: 394
Effective search space:   158388
Effective search space used:   158388
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 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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