GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Burkholderia phytofirmans PsJN

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

Query= BRENDA::A0A140N9B6
         (406 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS15580 BPHYT_RS15580
           acetylornithine aminotransferase
          Length = 394

 Score =  281 bits (720), Expect = 2e-80
 Identities = 160/382 (41%), Positives = 226/382 (59%), Gaps = 7/382 (1%)

Query: 9   NFDEWMIP----VYASAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREAL 64
           NF+E+ I     +      +   G+GS L+D  GK Y+DF  G AVN+LGH +  + EAL
Sbjct: 2   NFNEYPIESLMYITNRPEIVFTHGKGSWLYDNNGKRYLDFIQGWAVNSLGHCNDGMIEAL 61

Query: 65  NEQASKFWHTGNGYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRY 124
           N+Q+    +    + N+P+ +LA  L   +  D+VFF NSGAEANE A+KLARK+   ++
Sbjct: 62  NKQSQLLINPSPAFYNQPMAQLAGLLTQHSCFDKVFFANSGAEANEGAIKLARKWGK-KF 120

Query: 125 GSHKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALIDDST 184
                 I+ F ++FHGRTL T+SA G+P +   +AP       A  NDI S   LI+  T
Sbjct: 121 KDGAFEIITFDHSFHGRTLATMSASGKPGWDTIYAPQVPGFPKADLNDIASVEKLINAKT 180

Query: 185 CAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVT 244
            AV++EPIQGEGGV+PA+  F+Q LREL  +HN LLI DEVQ+G GR G L+AY    + 
Sbjct: 181 VAVMLEPIQGEGGVIPATREFMQQLRELTKKHNLLLIVDEVQSGCGRAGTLFAYELSDIE 240

Query: 245 PDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEM 304
           PD++T  K +GGG P+ ALLA  E A V   G  G TY GNPL +AV   V+  +  P  
Sbjct: 241 PDIMTLGKGIGGGVPLAALLAKAEIA-VFEAGDQGGTYNGNPLMTAVGYSVISQLTAPGF 299

Query: 305 LNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVM 364
           L G++ R ++   +L  ++   G F   RG GLL   +L  D   Q  + +++    G++
Sbjct: 300 LEGLRARGEYLRAKLLELSEERG-FEGERGEGLLRALLLGKDIGNQIVEKARDMQPDGLL 358

Query: 365 VLIAGGNVVRFAPALNVSEEEV 386
           +  A  N++RF PALNV+ EE+
Sbjct: 359 LNAARPNLLRFMPALNVTNEEI 380


Lambda     K      H
   0.319    0.135    0.406 

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: 430
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 preprint on GapMind for carbon sources, or view the source code.

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