GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Clostridium acetobutylicum ATCC 824

Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_014518834.1 CA_RS02090 aspartate aminotransferase family protein

Query= SwissProt::O50131
         (454 letters)



>NCBI__GCF_000008765.1:WP_014518834.1
          Length = 426

 Score =  308 bits (789), Expect = 2e-88
 Identities = 171/412 (41%), Positives = 247/412 (59%), Gaps = 20/412 (4%)

Query: 38  LVIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIKKQLDLVLHAAGTDYYNP 97
           L + R EG Y    DG  +LDF+SG+ V N+G  NP VI+A K+Q+D ++H      Y  
Sbjct: 22  LGVVRGEGAYLYTEDGRKVLDFASGVAVCNLGHNNPAVIKAAKEQMDKLIHGGHNVVYYE 81

Query: 98  YQVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIAKWSTNRKMFIAFIGAFHGRTHG 157
             V+LA+K+VE+     +  V+ SNSG EANE A+K+AK+ T R+  I+F G+FHGRT  
Sbjct: 82  SYVKLAEKIVELTGN--KTMVYFSNSGAEANEGAIKLAKYITKRQAIISFKGSFHGRTLA 139

Query: 158 TMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGIDGYENPDELINRVIDYIEEYLFE 217
           T S+T S    R      +P V    YP  +R P+     +N +      I   E+ +F+
Sbjct: 140 TTSITGSSSKYRKNYEGLLPSVYFAEYPYCFRCPYK----QNKESCNMECISQFED-MFK 194

Query: 218 HYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLADKHGILLIDDEVQMGMGRTGRMW 277
             +  E VA I  EP+QGEGGY+VPPK F K ++++ DK+GI LI DEVQ G GRTG+++
Sbjct: 195 KLIEPESVAAIIMEPVQGEGGYIVPPKKFLKAVREICDKYGICLIFDEVQCGFGRTGKIF 254

Query: 278 AIEHFDIVPDIVTVAKALGGGIPIGATIFRADL-DFGVSGVHSNTFGGNTVAAAAALAVI 336
           A E+F++ PDI T AKA+  G P+ A I + +L +   +G H  TFGGN VA AA+LA I
Sbjct: 255 AHENFEVEPDIFTCAKAIASGFPLSAVIGKKELMEKWPAGAHGGTFGGNPVACAASLATI 314

Query: 337 EELQNGLIENAQKLEPLFRERLEEMKEKYEIIGDVRGLGLAWGVEFVKDRKTKEYATKER 396
           +EL++G+++NA  +    +E L ++K+KY  IGD+RG+GL  G+EF K+    +      
Sbjct: 315 KELESGVLDNANNMGNYLKEELLKLKDKYACIGDIRGIGLMIGMEFCKENNNPD------ 368

Query: 397 GEIVV----EALKRGLALLGCG--KSAIRLIPPLIISEEEAKMGLDIFEEAI 442
           G+IV      A+   L LLGCG   + +R I PL + + E  M + I E+ I
Sbjct: 369 GDIVTFIREVAVNNNLILLGCGTEHNVLRFIAPLTVEKSEIDMAISIVEKGI 420


Lambda     K      H
   0.319    0.139    0.410 

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: 523
Number of extensions: 24
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: 454
Length of database: 426
Length adjustment: 32
Effective length of query: 422
Effective length of database: 394
Effective search space:   166268
Effective search space used:   166268
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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