GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Lacinutrix algicola AKS293

Align Transaminase BacF; Transaminase A; EC 2.6.1.- (characterized)
to candidate WP_055435119.1 ASC41_RS02745 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::P39643
         (399 letters)



>NCBI__GCF_001418085.1:WP_055435119.1
          Length = 379

 Score =  255 bits (651), Expect = 2e-72
 Identities = 144/368 (39%), Positives = 211/368 (57%), Gaps = 3/368 (0%)

Query: 17  FSLVFQKVKEMEKTGAHIINLGQGNPDLPTPPHIVEALREASLNPSFHGYGPFRGYPFLK 76
           FS   ++V  +   G  IINLG G+PDL  P  ++ A+ E+  +   H Y  ++G P L+
Sbjct: 15  FSKKLKEVNSLILQGKPIINLGIGSPDLQPPGKVISAITESFKDGRAHKYQSYQGIPELR 74

Query: 77  EAIAAFYKREYGVTINPETEVALFGGGKAGLYVLTQCLLNPGDIALVPNPGYPEYLSGIT 136
           EAIA FYK  + V +N  TEV    G K G+  ++   LN GD  L+PNPGYP Y S   
Sbjct: 75  EAIAGFYKTHFQVDVNATTEVLPLMGSKEGIMHISMAFLNEGDAVLIPNPGYPTYTSVTK 134

Query: 137 MARAELYEMPLYEENGYLPDFEKIDPAVLEKAKLMFLNYPNNPTGAVADAAFYAKAAAFA 196
           + +AE     L  EN + P+ E+++   L K K+M+LNYP+ PTGA A  A +     FA
Sbjct: 135 LLQAEPIFYNLDTENNWCPNIEELEKQDLSKVKIMWLNYPHMPTGAKATKAVFESLITFA 194

Query: 197 KEHNIHLIHDFAYGAFEFDQKPASFLEAEDAKTVGAELYSFSKTFNMAGWRMAFAVGNEK 256
           K+H+I L++D  Y +F  +++P S L  E AK V  EL S SKTFNMAGWR+   +GN +
Sbjct: 195 KKHDILLVNDNPY-SFILNKEPLSILSIEGAKDVCLELNSLSKTFNMAGWRVGMLLGNNE 253

Query: 257 IIQAVNEFQDHVFVGMFGGLQQAASAALSGDPEHTESLKRIYKERIDFFTALCEKELGWK 316
           ++ AV + + ++  GMF G+QQ A  AL+       SL  IY++R      L  K L   
Sbjct: 254 LLNAVLKVKSNMDSGMFYGIQQGAIEALNSSKMWFVSLNNIYEKRRKLVWELATK-LNCS 312

Query: 317 MEKPKGTFYVWAEIPNTFETSHQFSDYLLEHAHVVVTPGEIFGSNGKRHVRISMVSKQED 376
            ++     +VWA++P     S  F D LL+  ++ +TPG IFGS G+ +VR S+ +  ++
Sbjct: 313 FDENATGLFVWAKLPAAL-NSEAFIDKLLKEHNLFITPGTIFGSQGEGYVRFSLCATVKE 371

Query: 377 LREFVTRI 384
           L E +TR+
Sbjct: 372 LEEAITRV 379


Lambda     K      H
   0.319    0.137    0.407 

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: 391
Number of extensions: 19
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: 399
Length of database: 379
Length adjustment: 30
Effective length of query: 369
Effective length of database: 349
Effective search space:   128781
Effective search space used:   128781
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 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