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:

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