GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Desulfovibrio vulgaris Hildenborough

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 207835 DVU2347 acetylornithine aminotransferase

Query= BRENDA::O30508
         (406 letters)



>MicrobesOnline__882:207835
          Length = 399

 Score =  304 bits (778), Expect = 3e-87
 Identities = 161/374 (43%), Positives = 221/374 (59%), Gaps = 5/374 (1%)

Query: 30  RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHVSNVFTNEPALRL 89
           R EGSR+WD  GRE ID   GIAVTSLGH HP L + +  QA+++ HVSN+F  E  L L
Sbjct: 29  RAEGSRMWDHEGREYIDLLSGIAVTSLGHCHPELAEVMARQARKLVHVSNLFYQEEQLDL 88

Query: 90  ARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTLFTV 149
           A KL+      + F  NSGAEANEAA KLARRY   V G   +E++  + +FHGRTL TV
Sbjct: 89  AEKLLSTLHCTKAFFCNSGAEANEAAIKLARRYMQRVRGVDAHEVVTLTGAFHGRTLATV 148

Query: 150 NVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPIQGEGGVLPAQQAYL 209
              GQ ++ DGF P   G     + D++AL+AAI+  T  V++E +QGEGGV P  Q Y 
Sbjct: 149 AATGQERFQDGFAPMPAGFRQAEWGDIDALRAAITPATAGVLVEMVQGEGGVRPMTQDYA 208

Query: 210 EGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGGFPIGAMLTT 269
                LC E   LL+ DE+Q+G+ R G  +A+ HYGV PDI++SAK+L  G P+GAM+TT
Sbjct: 209 RAVADLCREKGVLLMVDEIQTGLCRTGRFWAHQHYGVEPDIVTSAKALANGLPMGAMMTT 268

Query: 270 GEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERFKSRLQKIGQEY 329
            E+A+    G+H TT+G   L S+VA A LD++    + +   A   R   R + IG + 
Sbjct: 269 DEVAQGFVAGSHATTFGAGALVSSVAAATLDIMKRDRLDERATAVGGRAMERFRAIGAKL 328

Query: 330 -GIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDVVRFAPSLVIDDAE 388
            G  +E+RG GL+IG  LT  + GK  +V         +       V+R  P+L ID+A+
Sbjct: 329 PGTIEEVRGYGLMIGIVLT--FSGK--EVWKELVARGFVCNNTQEKVLRLVPALTIDEAD 384

Query: 389 IDEGLERFERAVAK 402
           +    +  E  +A+
Sbjct: 385 LTAFADTLEDILAR 398


Lambda     K      H
   0.318    0.135    0.394 

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: 401
Number of extensions: 15
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: 406
Length of database: 399
Length adjustment: 31
Effective length of query: 375
Effective length of database: 368
Effective search space:   138000
Effective search space used:   138000
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: 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