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_3630 N515DRAFT_3630 4-aminobutyrate aminotransferase

Query= curated2:Q97GH9
         (387 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3630
          Length = 469

 Score =  153 bits (386), Expect = 1e-41
 Identities = 113/428 (26%), Positives = 198/428 (46%), Gaps = 68/428 (15%)

Query: 17  FDKGEGTKLYDKDGNEYIDFVSGVAVNCLGHCNPSIVKAIEEQSSKLMHVSNYYWNENAM 76
           F  G+G+ +YD  G  ++D     +    G+ N  +   ++ Q   L  V++ Y ++  +
Sbjct: 41  FRHGQGSWMYDTAGVPFLDLQMWYSAVNFGYGNKRLNDTLKAQIDTLPQVASQYLHQTRI 100

Query: 77  ELTEILCKNSEFD-----KVFMCNSGTEAIEAGLKLARKYALLHGDENKKEIIY-MDNSF 130
           EL + +  +++       +V     G +A+E  LKL R Y      +N K +++  +  +
Sbjct: 101 ELAKTIAVDAQQKFGLKGRVHFNVGGAQAVEDSLKLVRNY------KNGKSLMFAFEGGY 154

Query: 131 HGRTMGALSVTGQPKYQESFKPL-------------------------------IGAVKS 159
           HGRT+GA S+T   +Y+  F                                     +  
Sbjct: 155 HGRTLGASSITSSYRYRRRFGHFGERAMFIPFPYPFRRPKGMTPEEYSDACVRQFERLFE 214

Query: 160 VKFNDLDDIKQKISSKTAAVIVEPIQGEGGIIPAKKEYLKLLRDLCDENNALLIFDEVQC 219
            ++N + D K    ++ AA  VEPIQG GG +   K + K L+ + D+   L++ DE+Q 
Sbjct: 215 TEYNGVWDPKVN-QAEYAAFYVEPIQGTGGYVIPPKNFFKDLKKVLDKYGILMVVDEIQM 273

Query: 220 GMGRVGSLFAYQKFEVVPDIVCIAKALGGGF-PIGAMLAKESVASS--FVPGDHGNTYGG 276
           G  R G L++ + F V PDI+   KAL  G  P+  + A+E + +   F PG   +T+  
Sbjct: 274 GFWRTGKLWSIEHFGVTPDIIVFGKALTNGLNPLSGLWAREEMINPEIFPPGSTHSTFNS 333

Query: 277 NPLACAVAIAVLKELVDKKVVEINVNEKSKYLFDKLMTLKEKYKVINDVRGMGLLIGVEV 336
           NPL  ++ + V+K +  +   E NV +K  +  D L  L++++K I DV G+GL +  E+
Sbjct: 334 NPLGTSLGLEVIK-MGYELDYETNVAKKGAHFLDALKDLQKRHKEIGDVDGLGLALRAEI 392

Query: 337 ACDVKKIINKCFESKL-----------------LLITAG---KNVVRFLPPLNVSFEEID 376
             D     NK    ++                 L++  G   KNV+ F P L+++ EEID
Sbjct: 393 CTDDGFTPNKALLDRMVDIGLAGDLEHNGKKIGLVLDVGGWYKNVITFAPSLDITHEEID 452

Query: 377 KALGIFEE 384
            A+ + ++
Sbjct: 453 LAIALLDQ 460


Lambda     K      H
   0.318    0.137    0.395 

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: 393
Number of extensions: 20
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 387
Length of database: 469
Length adjustment: 32
Effective length of query: 355
Effective length of database: 437
Effective search space:   155135
Effective search space used:   155135
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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