GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Salinicoccus carnicancri Crm

Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_017549848.1 C792_RS0112765 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q9RAT0
         (391 letters)



>NCBI__GCF_000330705.1:WP_017549848.1
          Length = 387

 Score =  328 bits (840), Expect = 2e-94
 Identities = 169/385 (43%), Positives = 243/385 (63%), Gaps = 7/385 (1%)

Query: 4   LKKFNPNLDKIEISLIRQFDQQVSSIPDIIKLTLGEPDFYTPEHVKQAGIAAIENNQSHY 63
           + K N  +  IE+   RQF  +V   P  + LTLG+PDF T + +++A I AI      Y
Sbjct: 1   MPKANRRMQYIEVPGTRQFANRVEEFPGCVDLTLGQPDFETSQPIREAAIDAINTQSMKY 60

Query: 64  TGMAGLLELRQAASEFLLKKYGLSYAAEDEILVTVGVTEAISSVLLSILVAGDEVLIPAP 123
           +   GL  LR+A S +   ++G  Y    E+LVTVG +E I  VL +IL  GDEV++PAP
Sbjct: 61  SHNTGLYVLREAISNYYKDRHGAHYDPNGEVLVTVGGSEGIDGVLRAILDPGDEVIVPAP 120

Query: 124 AYPGYEPLITLAGGSLVEIDTRANDFVLTPEMLDQAIIEREGKVKAVILNYPANPTGVTY 183
            Y GYEP+I L+GG    +DT     + TPE++++ I E   K KAV+LNYP NPTGVTY
Sbjct: 121 TYLGYEPIIELSGGITKFVDTTDTGLIATPELIERNITE---KTKAVLLNYPTNPTGVTY 177

Query: 184 NREQIKDLAEVLKKHEVFVIADEVYSELNYTDQPHVSIAEY--APEQTIVLNGLSKSHAM 241
            +EQ+  L EV +K+++FVI DE+Y E N  +  H+S+A Y    E+ +V+NGLSKSH M
Sbjct: 178 TKEQMDRLVEVFRKYDIFVITDEIYGE-NTLEGDHISLAGYPEIKEKVLVINGLSKSHGM 236

Query: 242 TGWRIGLIFAARELVAQIIKTHQYLVTSASTQSQFAAIEALKNGADDALPMKKEYLKRRD 301
           TGWRIG +   R+++ ++   H Y    AS  SQ+AAIEALK+       M KEY++RRD
Sbjct: 237 TGWRIGYVTGHRQIMEEVTAVHLYNTICASLPSQYAAIEALKHQLHVPGEMNKEYIRRRD 296

Query: 302 YIIEKMSALGFKIIEPDGAFYIFAKIPADLEQDSFKFAVDFAKENAVAIIPGIAFGQYGE 361
           YI ++++ +G ++ +P GAFYIF  +    E DSFKF  +  +   +A++PG +F ++GE
Sbjct: 297 YIYDRLTGMGLEVKKPTGAFYIFPSV-EKYEHDSFKFCTELLETVQLAVVPGRSFSEFGE 355

Query: 362 GFVRLSYAASMDVIEQAMARLTDYV 386
           G +RLS+A SM  +E+A  RL  Y+
Sbjct: 356 GHIRLSFACSMHELEEAADRLEKYL 380


Lambda     K      H
   0.318    0.135    0.375 

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: 440
Number of extensions: 21
Number of successful extensions: 4
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: 391
Length of database: 387
Length adjustment: 30
Effective length of query: 361
Effective length of database: 357
Effective search space:   128877
Effective search space used:   128877
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 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