GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Azohydromonas australica DSM 1124

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_028997539.1 H537_RS0108305 amino acid aminotransferase

Query= BRENDA::W0PFQ7
         (399 letters)



>NCBI__GCF_000430725.1:WP_028997539.1
          Length = 399

 Score =  523 bits (1347), Expect = e-153
 Identities = 256/396 (64%), Positives = 308/396 (77%)

Query: 3   TLFNAVELAPRDPILGLNEQYNADTRDTKVNLGVGVYYDDNGKIPLLKAVQEAERQRVEA 62
           +LF AVE+APRDPILGLNEQ+ AD    KVNLGVGVY+DD GK+PLLK V  AE+Q +EA
Sbjct: 2   SLFAAVEMAPRDPILGLNEQFAADPNPAKVNLGVGVYFDDEGKLPLLKCVAAAEQQLLEA 61

Query: 63  HAARGYLPIEGIGNYNKGAQELLFGKDSDVITQGRALTFQALGGTGALKIGADFLKQLQP 122
              RGYLPI+GI  Y+K  Q L+FG DSD +  GR  T QALGGTG LKIGADFLK++ P
Sbjct: 62  KKPRGYLPIDGIAAYDKAVQGLVFGADSDAVKGGRVATVQALGGTGGLKIGADFLKRVNP 121

Query: 123 DSTVYISDPSWENHRALFERAGFKVETYSYYDAATHGLNFDGFAASVKAMPEGSIIVLHA 182
            + V ISDPSWENHRALF  AGF+V TY YYDA   G+ FD   A++++  +G+++VLHA
Sbjct: 122 GAKVLISDPSWENHRALFTNAGFEVGTYPYYDADKRGVRFDDMVAALRSAAKGTVVVLHA 181

Query: 183 CCHNPTGVDPSPEQWQQIATLVKERNLVPFLDIAYQGFGAGLQEDAAVVRLFADLGMSMF 242
           CCHNPTG D +PEQW Q+   VK+  LV FLD+AYQGFG G+ ED AV++ F D G+  F
Sbjct: 182 CCHNPTGYDITPEQWTQVVAAVKDAGLVAFLDMAYQGFGEGIAEDGAVIQQFLDAGIDFF 241

Query: 243 ISSSFSKSFSLYGERVGALTVVTSSTDEASRVLSQIKRVIRTNYSNPPTHGGMVVAQILN 302
           +S+SFSKSFSLYGERVGAL+VV  S DEA+RVLSQ+K VIRTNYSNPPT G  VVA +L 
Sbjct: 242 VSTSFSKSFSLYGERVGALSVVCDSADEAARVLSQLKIVIRTNYSNPPTFGAQVVATVLT 301

Query: 303 TPELFAQWESELAQMRDRIREMRKQLTDKLNAAGVKQDFNFVMAQRGMFSYSGLTKEQVE 362
           TP L AQWE ELA MR RI+ MR  L +KL AAGVKQD ++++ Q+GMFSYSGL KEQ++
Sbjct: 302 TPSLRAQWEEELAGMRQRIKLMRSLLVEKLQAAGVKQDLSYIVRQKGMFSYSGLGKEQMQ 361

Query: 363 RLRTEHGIYAVNSGRICVAALNSRNIDSVVKAIAAV 398
           RLR+E G+Y V+SGRICVAALNSRNID+V  A+A V
Sbjct: 362 RLRSEFGVYGVDSGRICVAALNSRNIDAVASAMAQV 397


Lambda     K      H
   0.318    0.134    0.385 

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: 486
Number of extensions: 17
Number of successful extensions: 1
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: 399
Length adjustment: 31
Effective length of query: 368
Effective length of database: 368
Effective search space:   135424
Effective search space used:   135424
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 25 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