GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Burkholderia phytofirmans PsJN

Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate BPHYT_RS15580 BPHYT_RS15580 acetylornithine aminotransferase

Query= CharProtDB::CH_002469
         (406 letters)



>FitnessBrowser__BFirm:BPHYT_RS15580
          Length = 394

 Score =  281 bits (719), Expect = 2e-80
 Identities = 156/359 (43%), Positives = 218/359 (60%), Gaps = 3/359 (0%)

Query: 28  GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEPVLRLA 87
           G+GS L+D  GK Y+DF  G AVN+LGH +  + EALN+Q+    +    + N+P+ +LA
Sbjct: 25  GKGSWLYDNNGKRYLDFIQGWAVNSLGHCNDGMIEALNKQSQLLINPSPAFYNQPMAQLA 84

Query: 88  KKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHGRTLFTVS 147
             L   +  D+VFF NSGAEANE A+KLARK+   ++      I+ F ++FHGRTL T+S
Sbjct: 85  GLLTQHSCFDKVFFANSGAEANEGAIKLARKWGK-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    + PD++T  K +GGG P+ ALLA  
Sbjct: 204 QLRELTKKHNLLLIVDEVQSGCGRAGTLFAYELSDIEPDIMTLGKGIGGGVPLAALLAKA 263

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

Query: 328 LFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEEEV 386
            F   RG GLL   +L  D   Q  + +++    G+++  A  N++RF PALNV+ EE+
Sbjct: 323 -FEGERGEGLLRALLLGKDIGNQIVEKARDMQPDGLLLNAARPNLLRFMPALNVTNEEI 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: 433
Number of extensions: 19
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:

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