GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Dyella japonica UNC79MFTsu3.2

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Query= curated2:Q8TUE8
         (395 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1751
          Length = 467

 Score =  197 bits (500), Expect = 7e-55
 Identities = 138/410 (33%), Positives = 216/410 (52%), Gaps = 54/410 (13%)

Query: 35  LVLSKGKGAVVQDIYGKEYIDCVAGIAVNNVGHCHPTVVKAIQAQAENLIHVSNLYYTEI 94
           L + +G+G  + D  G+ Y+D ++    N  GH +P +  A++ Q + L HV    +T  
Sbjct: 48  LPIVRGEGPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLEHVIFAGFTHE 107

Query: 95  QA-EFAETLASIT--GMERVFFCNSGAESVEAAMKLA------RVATGKSAFVAAEHSFH 145
            A E AE LA IT  G+ERVF  ++G+ ++E A+K++      + A  K+ F+A   S+H
Sbjct: 108 PAIELAERLAQITPAGLERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTRFIALTGSYH 167

Query: 146 GRTIGALSVTHKSMYRDPFMP--------PVSSETTFVPYSDAEA-----------IRQA 186
           G T+GALSV+  ++YR  + P        P        P   AEA           + + 
Sbjct: 168 GETLGALSVSDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACAARRLGELRVLLEQ 227

Query: 187 ISENTAAVILEP-IQGEGGINIPDPGYLKEVREICDETGALLIFDEVQTGFGRTGTWFCK 245
            +  T AVI+EP +Q  GG+ +  P YL  +R +CDE G   I DE+  GFGRTGT F  
Sbjct: 228 HAHETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEIAVGFGRTGTLFAC 287

Query: 246 EQFGVEPDIMSMSKAIGGGF-PMGAI--------AAHNGINFGRG-QHASTFGGGPLACA 295
           EQ GV PD M +SK + GGF P+ A+        A +   N G+   H+ ++ G PLAC 
Sbjct: 288 EQAGVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFLHSHSYTGNPLACR 347

Query: 296 AALASVKVIREEKLLERSKEMGAYFMKKLAGM-VRDDVVEVRGKGLMIGVEI-------- 346
           AALA++ + R+E +LER++E+ A+  ++LA +     V +VR  G++  VE+        
Sbjct: 348 AALATLDIFRDEPVLERNRELAAHLARRLAPLREHPQVADVRQTGMIAAVELVRDKATRA 407

Query: 347 KYPCG-----KFVDFAREQGVLVNCTSDSVLRLVPPLVITKEQIDTVVDV 391
            YP       +      E G L+     +V+  +PP V++ +++D +VDV
Sbjct: 408 PYPSEERRGLRVYLHGLEHGALLR-PLGNVVYFMPPYVVSTDELDHLVDV 456


Lambda     K      H
   0.319    0.135    0.391 

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: 416
Number of extensions: 18
Number of successful extensions: 6
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: 395
Length of database: 467
Length adjustment: 32
Effective length of query: 363
Effective length of database: 435
Effective search space:   157905
Effective search space used:   157905
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 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:

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