GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Lacinutrix algicola AKS293

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_055435119.1 ASC41_RS02745 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q8YTF2
         (403 letters)



>NCBI__GCF_001418085.1:WP_055435119.1
          Length = 379

 Score =  254 bits (650), Expect = 2e-72
 Identities = 131/378 (34%), Positives = 215/378 (56%), Gaps = 2/378 (0%)

Query: 9   ADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHG 68
           A+R+  +  Y F++  +       QG  +I+LG+G+PD   P  V+ A  ++ +D + H 
Sbjct: 4   ANRLHSVEEYYFSKKLKEVNSLILQGKPIINLGIGSPDLQPPGKVISAITESFKDGRAHK 63

Query: 69  YPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPS 128
           Y  ++G    R AI  +Y   + V ++  +E LPL+GSKEG+ H+++A++N GD VL+P+
Sbjct: 64  YQSYQGIPELREAIAGFYKTHFQVDVNATTEVLPLMGSKEGIMHISMAFLNEGDAVLIPN 123

Query: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188
           P YP +     +         L  EN+W  ++  + ++   K KI++ NYP  PTGA A 
Sbjct: 124 PGYPTYTSVTKLLQAEPIFYNLDTENNWCPNIEELEKQDLSKVKIMWLNYPHMPTGAKAT 183

Query: 189 REFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMA 248
           +  FE ++ FA+K++ILLV+D  Y+ +     +P S+L I GAKD+ +E ++LSKT+NMA
Sbjct: 184 KAVFESLITFAKKHDILLVNDNPYSFIL--NKEPLSILSIEGAKDVCLELNSLSKTFNMA 241

Query: 249 GWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDF 308
           GWRVG ++GN  ++  +  +K+N+D G+F  +Q  A  AL    ++   +   Y  RR  
Sbjct: 242 GWRVGMLLGNNELLNAVLKVKSNMDSGMFYGIQQGAIEALNSSKMWFVSLNNIYEKRRKL 301

Query: 309 LIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGYV 368
           + +   +L     +    +++W K P  + S  F   LL++  + +TPG  FG  GEGYV
Sbjct: 302 VWELATKLNCSFDENATGLFVWAKLPAALNSEAFIDKLLKEHNLFITPGTIFGSQGEGYV 361

Query: 369 RISLIADCDRLGEALDRI 386
           R SL A    L EA+ R+
Sbjct: 362 RFSLCATVKELEEAITRV 379


Lambda     K      H
   0.321    0.140    0.427 

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: 369
Number of extensions: 21
Number of successful extensions: 3
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: 403
Length of database: 379
Length adjustment: 31
Effective length of query: 372
Effective length of database: 348
Effective search space:   129456
Effective search space used:   129456
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: 50 (23.9 bits)

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

Links

Downloads

Related tools

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