GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Paraburkholderia bryophila 376MFSha3.1

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

Query= BRENDA::A0A140N9B6
         (406 letters)



>FitnessBrowser__Burk376:H281DRAFT_04057
          Length = 394

 Score =  290 bits (742), Expect = 5e-83
 Identities = 165/382 (43%), 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   NFNEYPIESLMYITNRPEIVFTHGKGSWLYDNNGKRYLDFIQGWAVNCLGHCDEGMIEAL 61

Query: 65  NEQASKFWHTGNGYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRY 124
           N+QA   ++    + NEP+ +LA  L   +  D+VFF NSGAEANE A+KLARK+   ++
Sbjct: 62  NQQAKLLFNPSPAFYNEPMAKLAALLTQHSCFDKVFFANSGAEANEGAIKLARKWGK-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   GV 
Sbjct: 181 VAVMLEPIQGEGGVIPATREFMQQLRELTRKHNVLLIVDEVQSGCGRAGTLFAYELSGVE 240

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

Query: 305 LNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVM 364
           L GV+ R ++   +L  ++   G F   RG GLL   +L  D   Q  + +++    G++
Sbjct: 300 LEGVRARGEYLRAKLLELSEERG-FKGERGEGLLRALLLGKDIGNQIVEKARDMQPDGLL 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: 431
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 Sep 17 2021. The underlying query database was built on Sep 17 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