GapMind for Amino acid biosynthesis

 

Aligments for a candidate for PPYAT in Cupriavidus basilensis 4G11

Align Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized)
to candidate RR42_RS35305 RR42_RS35305 aspartate aminotransferase

Query= SwissProt::H3ZPU1
         (389 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS35305 RR42_RS35305 aspartate
           aminotransferase
          Length = 401

 Score =  224 bits (572), Expect = 3e-63
 Identities = 134/397 (33%), Positives = 224/397 (56%), Gaps = 22/397 (5%)

Query: 1   MALSDRLEMVNPSEI----RKLFDLAQGIEGIISLGIGEPDFDTPEHIKEYAKEALDKGL 56
           ++L+DRL  + PS      +++ +L      +I L  GEPDF+TP HI+E A  A+  G 
Sbjct: 2   LSLTDRLNRIKPSPSSMAGQRVRELRAAGRDVIGLTAGEPDFETPAHIREAAWRAMQAGK 61

Query: 57  THYSPNIGILELREAVAEKFKKHNGIDADPKTQIMITVGTNQQILMGLATFLKDNEEVLI 116
           T Y+   G  ELR A A+KFK+ NG+D    ++I+++ G  Q I   L   ++  +EV++
Sbjct: 62  TRYTDVGGTAELRHAAAQKFKRENGLDY-AASEIIVSTGAKQVIFNALMCTVQQGDEVIV 120

Query: 117 PSPMFVSYAPAVILAGGKPVEVPTYEENEFRLSVDELEKYVTPKTRALIINTPNNPTGAV 176
           P+P +VSY    + AGG PV V    EN F+L+ +ELE+ ++ +TR LI+N+PNNP+GA 
Sbjct: 121 PAPYWVSYPDITLFAGGVPVFVACQAENGFKLTPEELERAISARTRWLILNSPNNPSGAA 180

Query: 177 LTKKDLEEIADFAVEH-DLMILSDEVYEYFVYDGVKNYSIA-SLDGMFERTITMNGFSKT 234
            T+ +L  IA+    H  + +++D++YE+  YDG    ++A +   +  RT+T+NG SK 
Sbjct: 181 YTRTELVAIAEVLERHPHVWVMTDDIYEHLTYDGAAFVTLAQAAPSLKARTLTINGVSKA 240

Query: 235 FAMTGWRLGFLAAPEWVVEKMVRFQMYNATCPVTFIQYAAAKALRDERSWQAVEEMRREY 294
           +AMTGWR+G+  AP  +++ MV+ Q  + +      Q AA  AL   + + A    +  +
Sbjct: 241 YAMTGWRIGYAGAPAPLIKAMVKLQSQSTSGANAVAQAAAIAALDGPQDFIAAN--KAVF 298

Query: 295 ERRRNLVWKRLNEM-GLPTVKPKGAFYIFPRIK----------DTGLSSKEFSELMIKEA 343
           + RR+ V   L ++ G+    P GAFY+F   +              SS ++   ++   
Sbjct: 299 QARRDRVVAALGQVDGIHCQAPAGAFYVFASCEALIGARTPHGSVIRSSDDWVNWVLDSQ 358

Query: 344 KVVVVPGSAFGQAGEGYVRISYATAYEKLEEAMDRME 380
            + V+ GSA+G   + + R+S+A +  +L+E   R+E
Sbjct: 359 DLAVLQGSAYGV--DTHFRLSFAASMAQLDEGCRRIE 393


Lambda     K      H
   0.318    0.135    0.387 

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: 334
Number of extensions: 15
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: 389
Length of database: 401
Length adjustment: 31
Effective length of query: 358
Effective length of database: 370
Effective search space:   132460
Effective search space used:   132460
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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