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

GapMind for Amino acid biosynthesis

Aligments 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for Amino acid biosynthesis