GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argD in Cupriavidus basilensis 4G11

Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate RR42_RS16955 RR42_RS16955 acetylornithine aminotransferase

Query= CharProtDB::CH_002469
         (406 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS16955 RR42_RS16955
           acetylornithine aminotransferase
          Length = 395

 Score =  292 bits (748), Expect = 1e-83
 Identities = 160/362 (44%), Positives = 223/362 (61%), Gaps = 9/362 (2%)

Query: 28  GEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEPVLRLA 87
           G+GS L D  GK Y+DF  G AVN LGH++  + +AL +Q+ K ++    + NEP+LRLA
Sbjct: 25  GKGSWLTDHNGKRYLDFVQGWAVNCLGHSNQAMIDALVDQSKKLFNPSPAFYNEPMLRLA 84

Query: 88  KKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSG---IVAFKNAFHGRTLF 144
           ++L DA+  D+VFF NSGAEANE A+KLARK+       HK+G   I+   ++FHGRTL 
Sbjct: 85  RQLTDASCFDKVFFANSGAEANEGAIKLARKWGR----KHKNGAFEIITMDHSFHGRTLA 140

Query: 145 TVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALIDDSTCAVIVEPIQGEGGVVPASNA 204
           T+SA G+  +   FAP       A  ND+ S   LI+D T A+++EP+QGEGGV+PAS  
Sbjct: 141 TMSASGKAGWDTIFAPQVPGFPKADLNDLASVEKLINDKTVAIMLEPVQGEGGVIPASRE 200

Query: 205 FLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLTTAKALGGGFPVGALL 264
           F+QGLR+L ++H  L I DEVQTG GR G ++AY   GV PD++T  K +GGG P+ ALL
Sbjct: 201 FMQGLRKLADQHKLLFIVDEVQTGCGRCGTMFAYELSGVEPDIMTLGKGIGGGVPLAALL 260

Query: 265 ATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVERLNTINH 324
              E A     G  G TY GNP+ +AV   V+  +  P  L  V+ +  +  E+L  +  
Sbjct: 261 CKAEVAS-FEAGDQGGTYNGNPVMTAVGSAVISQLTAPGFLQSVQDKGAYLREQLLALTS 319

Query: 325 RYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEE 384
            +GL  E RG GLL   VLN D   Q  + +++    G+++     N++RF PALNV+ E
Sbjct: 320 EFGLGGE-RGEGLLRALVLNKDIGPQLVEEARDMQPQGLLLNSPRPNLLRFMPALNVTIE 378

Query: 385 EV 386
           E+
Sbjct: 379 EI 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: 427
Number of extensions: 23
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: 395
Length adjustment: 31
Effective length of query: 375
Effective length of database: 364
Effective search space:   136500
Effective search space used:   136500
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