GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Pseudomonas simiae WCS417

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate GFF5065 PS417_25950 acetylornithine aminotransferase

Query= curated2:Q89RB7
         (404 letters)



>FitnessBrowser__WCS417:GFF5065
          Length = 420

 Score =  211 bits (537), Expect = 3e-59
 Identities = 133/378 (35%), Positives = 191/378 (50%), Gaps = 11/378 (2%)

Query: 26  VLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRAFHNDQL 85
           V  RG+G W+WD+D   YLD     +A S GH    ++ A+ +Q   L       HN   
Sbjct: 38  VFVRGQGSWLWDSDDRAYLDFSQGNAANSLGHSPQVLIKALADQTQALINPGNGLHNRAQ 97

Query: 86  APFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCADNFHGR 145
               E +   TGS +   +NSGAEAVE+AIK  RKWG   +G       II  +   HGR
Sbjct: 98  LNLAERLCHRTGSDQAYLLNSGAEAVEAAIKLARKWGQLHRG---GAYRIISASAGSHGR 154

Query: 146 TLGIVGFSTD-PETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGEAGVII 204
           +   +  S   PE R  F P  PGF  +PF D +AL  A+   TVA L+EPIQGEAGVI 
Sbjct: 155 SFAAMSASAGGPENR--FEPQLPGFSHVPFNDLSALHAAVDAQTVAILLEPIQGEAGVIP 212

Query: 205 PPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALAGGFYP 264
               Y   V  LC    ++L+LDE+QTG+GR G LLAEQ  G+ AD+  LGK L GG  P
Sbjct: 213 ATEHYLKGVERLCRELGILLILDEVQTGIGRCGTLLAEQQYGVRADIITLGKGLGGG-VP 271

Query: 265 VSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGARLLEGL 324
           ++A+L+  +       G+   T  GN L  +   A +  ++E G +++    G  L EGL
Sbjct: 272 LAALLARGKAC-CFEVGELEGTHHGNALMASAGLAVLEAVLEHGFMDHVRESGLYLGEGL 330

Query: 325 KDIRANTVR-EVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTIRIAPPLVI 383
             +       ++RG GLM  + L  ++  A    +A   +G++      + +R  P L +
Sbjct: 331 ARLAYRYDHGQLRGHGLMWGLTLSDDSADA--VVKAALHEGLIINAPQPNCLRFTPALTV 388

Query: 384 TSDEVDWALEQFATTLTQ 401
           +   +D  L + A   ++
Sbjct: 389 SKSNIDEMLLRLARAFSR 406


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: 442
Number of extensions: 16
Number of successful extensions: 3
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: 420
Length adjustment: 31
Effective length of query: 373
Effective length of database: 389
Effective search space:   145097
Effective search space used:   145097
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