GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Salinicoccus carnicancri Crm

Align Transaminase BacF; Transaminase A; EC 2.6.1.- (characterized)
to candidate WP_017548713.1 C792_RS0106810 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::P39643
         (399 letters)



>NCBI__GCF_000330705.1:WP_017548713.1
          Length = 384

 Score =  260 bits (664), Expect = 5e-74
 Identities = 134/354 (37%), Positives = 207/354 (58%), Gaps = 3/354 (0%)

Query: 34  IINLGQGNPDLPTPPHIVEALREASLNPSFHGYGPFRGYPFLKEAIAAFYKREYGVTINP 93
           ++NL  G PD  TP  I +A+ ++   P    YG FRG    K+AI   YK+ Y VT++ 
Sbjct: 29  LLNLAVGIPDGETPDVIKKAVADSVYLPENQRYGVFRGKRSFKDAIIRLYKKHYDVTLHE 88

Query: 94  ETEVALFGGGKAGLYVLTQCLLNPGDIALVPNPGYPEYLSGITMARAELYEMPLYEENGY 153
           E  +AL  G K+GL       + PG+   +PNPGYP+Y++G+ +AR E+Y++PL   N +
Sbjct: 89  EN-IALLYGTKSGLVQFPMTFIEPGEGVYLPNPGYPDYMAGVKLARGEIYDLPLLAGNDF 147

Query: 154 LPDFEKIDPAVLEKAKLMFLNYPNNPTGAVADAAFYAKAAAFAKEHNIHLIHDFAYGAFE 213
           LPDF+ +D   L  A+L++LNYP+NP GAVA   F+ +     +     ++HDFAY AF 
Sbjct: 148 LPDFDSLDKDELSNARLIYLNYPSNPLGAVATKEFFDETVERFRGTRTRIVHDFAYAAFS 207

Query: 214 FDQKPASFLEAEDAKTVGAELYSFSKTFNMAGWRMAFAVGNEKIIQAVNEFQDHVFVGMF 273
           FD+K  S L ++ +     E+YS SK FNM+G+R+ FAVGN+++++++N +QDH   GM+
Sbjct: 208 FDEKHPSILSSDPSLECCMEIYSLSKGFNMSGFRVGFAVGNKEMVESINLYQDHTQTGMW 267

Query: 274 GGLQQAASAALSGDPEHTESLKRIYKERIDFFTALCEKELGWKMEKPKGTFYVWAEIPNT 333
           G LQ A+ AAL  + E        +++R DFF      E G  +   KG  + W  +P  
Sbjct: 268 GVLQDASVAALEHEEEILSMQHVKFQKRRDFFEK-AVIESGIPLNPLKGGIFGWIAVPKG 326

Query: 334 FETSHQFSDYLLEHAHVVVTPGEIFGSNGKRHVRISMVSKQEDLREFVTRIQKL 387
           ++    F+D+L+    ++VTPG  FGS GK ++RIS+      L   + R+  +
Sbjct: 327 YD-GESFADFLIREKSILVTPGRPFGSRGKNYIRISLAVDDAVLDAVIERLDTI 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: 458
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: 384
Length adjustment: 31
Effective length of query: 368
Effective length of database: 353
Effective search space:   129904
Effective search space used:   129904
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.

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