GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Cupriavidus basilensis 4G11

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

Query= BRENDA::A0A140N9B6
         (406 letters)



>FitnessBrowser__Cup4G11:RR42_RS16955
          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    0.135    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: 423
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 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