GapMind for Amino acid biosynthesis

 

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

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate N515DRAFT_3307 N515DRAFT_3307 glutamate-1-semialdehyde 2,1-aminomutase

Query= BRENDA::Q9FNK4
         (475 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3307
          Length = 426

 Score =  142 bits (357), Expect = 3e-38
 Identities = 101/310 (32%), Positives = 152/310 (49%), Gaps = 31/310 (10%)

Query: 59  PVVFSRANGSTIWDPEGKRYIDFLAAYSAVNQGHCHPKIMKALQEQVEKLTLSSRAFYND 118
           P   +RA+G+ +WD EGKRYID++ ++  +  GH HP++ +A++  V+         +  
Sbjct: 32  PFFTARADGAYLWDVEGKRYIDYVGSWGPMIVGHNHPRVREAVERAVK-----DGLSFGT 86

Query: 119 KFPV---FAERLTNMF-GYDMVLPMNTGAEGVETALKLARKWGHEKKNIPKDEAIIVSCC 174
             P     AE +T +    DMV  +N+G E   +A++LAR      K        IV   
Sbjct: 87  PCPAEITMAETITRLVPSVDMVRMVNSGTEATMSAIRLARGATGRSK--------IVKFE 138

Query: 175 GCFHGRTLAIVSMSCDNDATRGFGPLLPG--------NLKVDFGDADSLEKIFKEKGDRI 226
           GC+HG   + +  +     T G  P  PG         L + + D  + E +F E G  I
Sbjct: 139 GCYHGHGDSFLVKAGSGALTFGV-PTSPGVPKAAADLTLTLAYNDLAAAEALFAEHGADI 197

Query: 227 AGFLFEPIQGEAGVIIPPDGYLKAVRELCTKYNVLMIADEVQSGLARSGKMLACDWEEIR 286
           AG + EP+ G    I P DGYL+ +R LCT++  L+I DEV +G  R     A     I 
Sbjct: 198 AGLIIEPVAGNMNCIPPKDGYLQGLRALCTRHGALLIFDEVMTGF-RVALGGAQAHYGIT 256

Query: 287 PDMVILGKALGGGVIPVSAVLADKDVMLHIKPG---QHGSTFGGNPLASAVAMASLDVIV 343
           PD+   GK +GGG +PV A    +++M  I P        T  GNP+A A  +A L++I 
Sbjct: 257 PDLSTFGKIIGGG-MPVGAYGGRRELMEQIAPAGPIYQAGTLSGNPVAMAAGLAMLELIQ 315

Query: 344 EEKLVERSAS 353
           E    +R A+
Sbjct: 316 EAGFYDRLAA 325


Lambda     K      H
   0.318    0.136    0.400 

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: 20
Number of successful extensions: 5
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: 475
Length of database: 426
Length adjustment: 33
Effective length of query: 442
Effective length of database: 393
Effective search space:   173706
Effective search space used:   173706
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