GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Azospirillum brasilense Sp245

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase

Query= BRENDA::Q98TS5
         (439 letters)



>FitnessBrowser__azobra:AZOBR_RS19630
          Length = 428

 Score =  208 bits (530), Expect = 2e-58
 Identities = 141/415 (33%), Positives = 220/415 (53%), Gaps = 50/415 (12%)

Query: 58  LPVALERGKGVYVWDVEGRRYFDFLSAYSAVNQGHCHPKILDALKSQADKLTLTSRAFYN 117
           +PV ++R +   +WDVEG R+ DF    + +N GH HPKI++A+K+Q D+ T T      
Sbjct: 22  MPVYVDRAENAELWDVEGNRFIDFAGGIAVLNTGHRHPKIIEAVKAQLDRFTHTCA---- 77

Query: 118 DVLGEYEEYITKIFGYNKVLP---------MNTGVEGGETACKLARKWAYTVKGIPKYKA 168
            ++  YE ++T     N ++P           TG E  E A K+AR  A+T  G P    
Sbjct: 78  -MVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKIAR--AHT--GRPG--- 129

Query: 169 QIIFAAGNFWGRTMSAISSSTDPSSYE-GFGPFMPGFKIIPY----------NDLPALER 217
            +I  +G F GRT+ A++ +     Y+ GFGPF       P+          + L ALE+
Sbjct: 130 -VIAFSGAFHGRTLLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQDSLKALEQ 188

Query: 218 ALQDP----NVAAFMVEPIQGEAGVIVPDEGYLTGVRQLCTAHNVLFIADEVQTGLARTG 273
             +       VAA +VEP+QGE G  +    +L  +R++C  + +L I DE+QTG ARTG
Sbjct: 189 LFKSDVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEIQTGFARTG 248

Query: 274 KMLAVDHENVRPDLVILGKALSGGVYPVSAVLCDDEVMLTIKPGEHGSTYGGNPLGCRVA 333
           KM A++H  V PDL+ + K+L+GG +P+SAV    E+M    PG  G TY G+PL    A
Sbjct: 249 KMFAIEHSGVEPDLMTMAKSLAGG-FPLSAVTGKAEIMDAPIPGGIGGTYAGSPLATTAA 307

Query: 334 MASLEVIEEEKLAENANXMGELL----RAELMKTPSDIVTAVRGKGLLNAIVIKQSKDCD 389
           +A L+VIEEEKL + +N +GE +    R    +    ++  VR  G + A+ + + +   
Sbjct: 308 LAVLDVIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMELVKDRGTK 367

Query: 390 ------AWKVCLRLRDNG--LLAKPTHGDIIRLAPPLTIKEDEIRECSEIIHKTL 436
                    +  +  + G  LL+  T+G++IR+  PLT  +  + E  +II ++L
Sbjct: 368 EPAAELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIERSL 422


Lambda     K      H
   0.318    0.136    0.404 

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: 441
Number of extensions: 23
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: 439
Length of database: 428
Length adjustment: 32
Effective length of query: 407
Effective length of database: 396
Effective search space:   161172
Effective search space used:   161172
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