GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Dechlorosoma suillum PS

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase

Query= curated2:Q89RB7
         (404 letters)



>FitnessBrowser__PS:Dsui_0023
          Length = 396

 Score =  229 bits (584), Expect = 1e-64
 Identities = 140/370 (37%), Positives = 196/370 (52%), Gaps = 7/370 (1%)

Query: 25  VVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRAFHNDQ 84
           +V + G G W+ D  G RYLD +  ++    GH HP I+ A+  QA +L   S AF+N+ 
Sbjct: 23  LVFAEGRGSWLVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGKLINPSPAFYNEP 82

Query: 85  LAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCADNFHG 144
                  +AA +   +V   ++GAEA E AIK  RKWG + KG      EII  A  FHG
Sbjct: 83  SLKLAAGLAAHSCFDRVFFASTGAEANEGAIKLARKWGQKHKG---GAHEIITFAGGFHG 139

Query: 145 RTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGEAGVII 204
           RTL  +  S  P     F P  PGF      D  ++   I   TVA ++EPIQGE GV+ 
Sbjct: 140 RTLATMSASGKPGWDTLFAPQVPGFPKAQLNDLDSVAALINERTVAIMLEPIQGEGGVVP 199

Query: 205 PPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALAGGFYP 264
             A +   +R++C    ++L++DE+QTG+GRTGKL A QH GIE D+  LGK + GG  P
Sbjct: 200 ASAEFLQLLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHAGIEPDIMTLGKGIGGG-VP 258

Query: 265 VSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGARLLEGL 324
           +SA+L+   V      G  G T+ GNPL  AV  A + VL   G +   A +G  L  GL
Sbjct: 259 LSALLAKESVC-CFEAGDQGGTYNGNPLMTAVGAAVLEVLTAPGFLAEVAAKGEYLGAGL 317

Query: 325 KDIRANT-VREVRGRGLMLAVELHPEAGRARRYCEALQG-KGILAKDTHGHTIRIAPPLV 382
           + +     +R  RG+GL+ A+ L  E G A       +G +G+L      H +R  P L 
Sbjct: 318 QRLSDRLGLRGERGQGLLRALLLADERGPAIVEAARERGPEGLLLNAPRPHLLRFMPSLT 377

Query: 383 ITSDEVDWAL 392
           ++ +E+D  L
Sbjct: 378 VSREEIDQML 387


Lambda     K      H
   0.319    0.136    0.405 

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: 406
Number of extensions: 21
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: 404
Length of database: 396
Length adjustment: 31
Effective length of query: 373
Effective length of database: 365
Effective search space:   136145
Effective search space used:   136145
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 (21.8 bits)
S2: 50 (23.9 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