GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Acidovorax sp. GW101-3H11

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= curated2:Q5HJI8
         (394 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4179
          Length = 459

 Score =  198 bits (503), Expect = 3e-55
 Identities = 137/407 (33%), Positives = 206/407 (50%), Gaps = 49/407 (12%)

Query: 21  LVISKGKGVKVWDTDGKQYIDCISGFSVANQGHCHPTIVKAMTEQASKLSIISRVLYSDN 80
           L I K +  ++WD +G+++ID   G +V N GH H  ++ A+  Q   L + +   +   
Sbjct: 55  LFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGVIAAVKAQ---LDLYTHTCFQVV 111

Query: 81  LGKWEEKICHL-------AKKDKVLPLNSGTEAVEAAIKIARKWGSEVKGITDGQVEIIA 133
             +   ++C         A   K L L +G EAVE AIKIAR +          +  +IA
Sbjct: 112 AYEPYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIARAYTK--------RPGVIA 163

Query: 134 MNNNFHGRTLGSLSLSNHDA-YKAGFHPLLQGTTTVDFGD------IEQLTQAIS----- 181
               +HGRT  +L L+   A YK GF P    T    F +      +EQ   ++      
Sbjct: 164 FTGGYHGRTNLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSVEQALHSVELIFKN 223

Query: 182 ----PNTAAIILEPIQGEGGVNIPPKGYIQAVRQLCDKHQILLIADEIQVGLGRTGKWFA 237
                  AA I+EP+QGEGG  + P  +I  ++ L D++ ILLIADE+Q G GRTG WFA
Sbjct: 224 DIEPERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQTGAGRTGTWFA 283

Query: 238 MEWEQVVPDIYILGKALGGGLYPVSAVLANNDVMRVLTPGTHGSTFGGNPLAIAISTAAL 297
            E   V PD+    K+L GG +P++ V+   DVM    PG  G T+ G+P+A A S A +
Sbjct: 284 SEQWPVAPDLITTAKSLAGG-FPLAGVVGRADVMDAPAPGGLGGTYAGSPVACAASLAVI 342

Query: 298 DVLKDEQLVERSERLGSFLLKAL--LQLKHPSIKEIRGRGLFIGIEL-------NTDAA- 347
           +    E+L+ RS+ +G+ L+++L  L  + P+I ++RG G  + IEL         DAA 
Sbjct: 343 EAFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFENGDLSRPDAAL 402

Query: 348 --PFVDQLIQRG--ILCKDTHRTIIRLSPPLVIDKEEIHQIVAAFQD 390
               V +  +RG  +L   TH  +IR+  PL    E +H+ +A   D
Sbjct: 403 TKQVVAEAARRGLILLSCGTHGNVIRILVPLTASDELLHEGLAILAD 449


Lambda     K      H
   0.319    0.137    0.402 

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: 420
Number of extensions: 20
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: 394
Length of database: 459
Length adjustment: 32
Effective length of query: 362
Effective length of database: 427
Effective search space:   154574
Effective search space used:   154574
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