Alignments for a candidate for argD in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for argD in Pseudomonas simiae WCS417

Align Acetylornithine aminotransferase 2; ACOAT 2; EC 2.6.1.11 (uncharacterized)
to candidate GFF5065 PS417_25950 acetylornithine aminotransferase

Query= curated2:Q7WDN7
         (396 letters)



>FitnessBrowser__WCS417:GFF5065
          Length = 420

 Score =  348 bits (894), Expect = e-100
 Identities = 189/386 (48%), Positives = 254/386 (65%), Gaps = 4/386 (1%)

Query: 10  ALMEITARPDLVFVRGQGSWLEDHAGKRYLDFVQGWAVNTLGHCAPEMKRALAEQADKLM 69
           +LM   ARP  VFVRGQGSWL D   + YLDF QG A N+LGH    + +ALA+Q   L+
Sbjct: 27  SLMPCVARPPHVFVRGQGSWLWDSDDRAYLDFSQGNAANSLGHSPQVLIKALADQTQALI 86

Query: 70  NPSPAFYNLPSIELAQRLTSASCFDRVFFANSGAEANEGAIKLARKWGRVNRNGAYKIIT 129
           NP    +N   + LA+RL   +  D+ +  NSGAEA E AIKLARKWG+++R GAY+II+
Sbjct: 87  NPGNGLHNRAQLNLAERLCHRTGSDQAYLLNSGAEAVEAAIKLARKWGQLHRGGAYRIIS 146

Query: 130 MNHGFHGRTLATMSASGKPGWDTMFAPQVEGFPKAEINDLDSVRALIDAQTVAVMLEPVQ 189
            + G HGR+ A MSAS   G +  F PQ+ GF     NDL ++ A +DAQTVA++LEP+Q
Sbjct: 147 ASAGSHGRSFAAMSASAG-GPENRFEPQLPGFSHVPFNDLSALHAAVDAQTVAILLEPIQ 205

Query: 190 GEAGVIPATREFMQGLRKLADEHGILFIVDEVQTGMGRTGSLFAYQQFDVIPDIMTLAKG 249
           GEAGVIPAT  +++G+ +L  E GIL I+DEVQTG+GR G+L A QQ+ V  DI+TL KG
Sbjct: 206 GEAGVIPATEHYLKGVERLCRELGILLILDEVQTGIGRCGTLLAEQQYGVRADIITLGKG 265

Query: 250 IGGGIPLAALLAREEVCVFAHGDQGGTYNGNPLCAAVGVAVFDTITAPGFMEAAQARTRQ 309
           +GGG+PLAALLAR + C F  G+  GT++GN L A+ G+AV + +   GFM+  +     
Sbjct: 266 LGGGVPLAALLARGKACCFEVGELEGTHHGNALMASAGLAVLEAVLEHGFMDHVRESGLY 325

Query: 310 LSEGLLALSAKRGLRGERGMGLLRALVLDRDDAPAIVEAARMLAPEGLLLNAPRGNLLRF 369
           L EGL  L+ +      RG GL+  L L  D A A+V+AA     EGL++NAP+ N LRF
Sbjct: 326 LGEGLARLAYRYDHGQLRGHGLMWGLTLSDDSADAVVKAA---LHEGLIINAPQPNCLRF 382

Query: 370 MPALNVTEADMARMLEQLDGVIAAVR 395
            PAL V+++++  ML +L    + VR
Sbjct: 383 TPALTVSKSNIDEMLLRLARAFSRVR 408


Lambda     K      H
   0.321    0.137    0.403 

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: 419
Number of extensions: 18
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: 396
Length of database: 420
Length adjustment: 31
Effective length of query: 365
Effective length of database: 389
Effective search space:   141985
Effective search space used:   141985
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 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:

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original 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