GapMind for Amino acid biosynthesis

 

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

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Query= SwissProt::P18335
         (406 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1751
          Length = 467

 Score =  176 bits (447), Expect = 1e-48
 Identities = 129/403 (32%), Positives = 192/403 (47%), Gaps = 43/403 (10%)

Query: 29  VKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISNV-FTNEPAL 87
           V+G+G  + D  G+ Y+D          GH +P +  ALK Q +TL H+    FT+EPA+
Sbjct: 51  VRGEGPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLEHVIFAGFTHEPAI 110

Query: 88  RLGRKLIEATFA--ERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRS 145
            L  +L + T A  ERV   ++G+ A E A K++ HY   + +  KT+ IA   ++HG +
Sbjct: 111 ELAERLAQITPAGLERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTRFIALTGSYHGET 170

Query: 146 LFTVSVGGQPKYSDGFGPKPADIIHVPFND-----------------LHAVKAVMDDH-- 186
           L  +SV     Y   + P     +  P  D                 L  ++ +++ H  
Sbjct: 171 LGALSVSDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACAARRLGELRVLLEQHAH 230

Query: 187 -TCAVVVEP-IQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHY 244
            TCAV+VEP +Q  GG+    P +L GLR LCD+     + DE+  G GRTG LFA    
Sbjct: 231 ETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEIAVGFGRTGTLFACEQA 290

Query: 245 GVTPDILTSAKALGGGF-PISAMLTTAEIASAFHPG-------SHGSTYGGNPLACAVAG 296
           GV+PD +  +K L GGF P+SA+LTT  +  AF+          H  +Y GNPLAC  A 
Sbjct: 291 GVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFLHSHSYTGNPLACRAAL 350

Query: 297 AAFDIINTPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAEL---------K 347
           A  DI     VLE  +         L  + +++   +D+R  G++   EL          
Sbjct: 351 ATLDIFRDEPVLERNRELAAHLARRLAPL-REHPQVADVRQTGMIAAVELVRDKATRAPY 409

Query: 348 PQYKGRARDFLYAGAEAGVMVLNAGPDVMRFAPSLVVEDADID 390
           P  + R       G E G ++   G +V+ F P  VV   ++D
Sbjct: 410 PSEERRGLRVYLHGLEHGALLRPLG-NVVYFMPPYVVSTDELD 451


Lambda     K      H
   0.322    0.138    0.415 

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: 460
Number of extensions: 23
Number of successful extensions: 7
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: 467
Length adjustment: 32
Effective length of query: 374
Effective length of database: 435
Effective search space:   162690
Effective search space used:   162690
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 (21.9 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