GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argD in Paraburkholderia bryophila 376MFSha3.1

Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate H281DRAFT_04057 H281DRAFT_04057 acetylornithine aminotransferase apoenzyme

Query= CharProtDB::CH_002469
         (406 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04057 H281DRAFT_04057
           acetylornithine aminotransferase apoenzyme
          Length = 394

 Score =  290 bits (741), Expect = 7e-83
 Identities = 161/359 (44%), Positives = 218/359 (60%), Gaps = 3/359 (0%)

Query: 28  GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEPVLRLA 87
           G+GS L+D  GK Y+DF  G AVN LGH    + EALN+QA   ++    + NEP+ +LA
Sbjct: 25  GKGSWLYDNNGKRYLDFIQGWAVNCLGHCDEGMIEALNQQAKLLFNPSPAFYNEPMAKLA 84

Query: 88  KKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHGRTLFTVS 147
             L   +  D+VFF NSGAEANE A+KLARK+   ++      I+ F ++FHGRTL T+S
Sbjct: 85  ALLTQHSCFDKVFFANSGAEANEGAIKLARKWGK-KFKDGAFEIITFDHSFHGRTLATMS 143

Query: 148 AGGQPAYSQDFAPLPADIRHAAYNDINSASALIDDSTCAVIVEPIQGEGGVVPASNAFLQ 207
           A G+P +   +AP       A  NDI S   LI+  T AV++EPIQGEGGV+PA+  F+Q
Sbjct: 144 ASGKPGWDTIYAPQVPGFPKADLNDIASVEKLINAKTVAVMLEPIQGEGGVIPATREFMQ 203

Query: 208 GLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAKALGGGFPVGALLATE 267
            LREL  +HN LLI DEVQ+G GR G L+AY   GV PD++T  K +GGG P+ ALLA  
Sbjct: 204 QLRELTRKHNVLLIVDEVQSGCGRAGTLFAYELSGVEPDIMTLGKGIGGGVPLAALLAKA 263

Query: 268 ECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVERLNTINHRYG 327
           E A V   G  G TY GNPL +AV   V+  +  P  L GV+ R ++   +L  ++   G
Sbjct: 264 EVA-VFEAGDQGGTYNGNPLMTAVGYSVISQLTAPGFLEGVRARGEYLRAKLLELSEERG 322

Query: 328 LFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEEEV 386
            F   RG GLL   +L  D   Q  + +++    G+++  A  N++RF PALNV+ EE+
Sbjct: 323 -FKGERGEGLLRALLLGKDIGNQIVEKARDMQPDGLLLNAARPNLLRFMPALNVTNEEI 380


Lambda     K      H
   0.319    0.136    0.407 

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: 434
Number of extensions: 17
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: 406
Length of database: 394
Length adjustment: 31
Effective length of query: 375
Effective length of database: 363
Effective search space:   136125
Effective search space used:   136125
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: 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