GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Pseudomonas fluorescens FW300-N2E3

Align acetylornithine transaminase (EC 2.6.1.11) (characterized)
to candidate AO353_10500 AO353_10500 acetylornithine aminotransferase

Query= BRENDA::A8J933
         (460 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_10500
          Length = 390

 Score =  311 bits (797), Expect = 2e-89
 Identities = 162/382 (42%), Positives = 227/382 (59%), Gaps = 10/382 (2%)

Query: 64  YVLQTYGRAPVVISHGKGAKMWDVEGKEYIDMAAGIAVNALGHSDSQWYAALVEQAEKLA 123
           Y++  Y R PV  S G+GA +WD  G EY+D  AG+AV +LGH++ +  AA+ EQA +L 
Sbjct: 7   YLMHNYARQPVSFSRGQGASLWDKHGVEYLDAIAGVAVTSLGHANPEIAAAIAEQAGQLL 66

Query: 124 HTSNLYHTQPQVELAKRLVENSFADKAFFCNTGTEANEGAIKFARKWARVRAGIDPYDGG 183
           HTSN++H + Q +L++RL   S   +AFFCN+G EANE A+K AR  A  R         
Sbjct: 67  HTSNMFHIEWQEQLSERLCALSGMQRAFFCNSGAEANEAALKLARLHANARH-------- 118

Query: 184 AVAPYELVSFTSCFHGRTMGALALTYKEQYKTPFYPMMPGHQLAEYNNLESAAAVIKKGK 243
            VA  +++   + FHGRT+  LA T     +  F P+MPG     Y+N+E    V  +  
Sbjct: 119 -VAQPQVLVMENSFHGRTLATLAATGNPAVQRGFEPLMPGFLRVPYDNIEEIRKVAAQSP 177

Query: 244 T-AAVFVEPVQGEGGVTPSTQAFLKGLRQLCDEAGALLVFDEVQCGLGRTGKLWGHQLFG 302
              AV VEPVQGEGGV  ++  +L+ LRQLCDE   L++ DEVQ G+GRTG  +G+Q  G
Sbjct: 178 DIVAVLVEPVQGEGGVHAASAGYLQALRQLCDEHDWLMMVDEVQTGMGRTGAWFGYQHAG 237

Query: 303 VEPDMMTLAKPLAGGLPIGTVLLKQHVADVMKPGDHGSTFAGNPLVCHVACSVFDIINSP 362
           + PD++TLAK L  G PIG  L +   A++  PG H STF GNPL C V C+V DI+   
Sbjct: 238 IVPDVITLAKALGNGFPIGACLARGKAAELFSPGHHASTFGGNPLACRVGCTVLDIMERD 297

Query: 363 AFLAAVEAKGERLRAGLRRTMAGNPHVQEVRGVGLLVGVQLDMMAGPVVDAARDMGVMAI 422
                    G RL A L+  +  +  V  +RG+GL+VG++L+     +V  A D   + I
Sbjct: 298 HIPQRAATSGRRLLAALQEALGNHSEVVSIRGLGLMVGIELNRQCAELVGRALDEQRLLI 357

Query: 423 TAGKGDVIRLVPPLVVTDAEID 444
           T  +G  +RL+PPL+  D++ID
Sbjct: 358 TVTRGTTLRLLPPLICEDSQID 379


Lambda     K      H
   0.319    0.134    0.396 

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: 439
Number of extensions: 16
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: 460
Length of database: 390
Length adjustment: 32
Effective length of query: 428
Effective length of database: 358
Effective search space:   153224
Effective search space used:   153224
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 (21.8 bits)
S2: 51 (24.3 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:

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