GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argD in Desulfovibrio vulgaris Hildenborough

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 208688 DVU3168 glutamate-1-semialdehyde-2,1-aminomutase

Query= curated2:P36839
         (385 letters)



>lcl|MicrobesOnline__882:208688 DVU3168
           glutamate-1-semialdehyde-2,1-aminomutase
          Length = 423

 Score =  152 bits (384), Expect = 2e-41
 Identities = 110/308 (35%), Positives = 160/308 (51%), Gaps = 17/308 (5%)

Query: 15  IKKAKGTYVEDQNGKTYLDFIQGIAVSNLGHCHEAVTEAVKKQLDSVWHVSNLFQNSLQE 74
           I +A G+ +   +G+T++DF++      LGH H  VT AV   +D         ++ +  
Sbjct: 37  IARAAGSRLHTVDGETFIDFVESWGPMLLGHTHPEVTAAVHAAVDRGTSYGAPCEDEVV- 95

Query: 75  QAAQKLAAHSAGDLVFFCNSGAEANEGAIKLARKATGKTKIITFLQSFHGRTYAGMAATG 134
            AA+ + A    D+V   NSG EA   A++LAR  TG+TK++ F+  +HG     +A+ G
Sbjct: 96  LAAKVVDALPGVDMVRMVNSGTEATMSALRLARGYTGRTKLVKFVGCYHGHADPFLASAG 155

Query: 135 QDKIKTGFGPMLGGFH--------YLPYNDPSAFKALG--EEGDIAAVMLETVQGEGGVN 184
              + T   P   G            PYND +A K L      DIAA+++E V G  G+ 
Sbjct: 156 SG-VATLSIPGTPGVPESTVRDTLLAPYNDLAAVKDLFALHGKDIAAIIVEAVAGNMGLV 214

Query: 185 PASAEFLSAVQSFCKEKQALLIIDEIQTGIGRTGKGFAYEHFGLSPDIITVAKGLGNGFP 244
           P  A FL  ++  C +  ALLI DE+ TG  R   G A + FG++PD+ T+ K +G G P
Sbjct: 215 PPKAGFLEGLRELCDQHGALLIFDEVITGF-RVSFGGAQQRFGITPDLTTLGKIIGGGLP 273

Query: 245 VGAVIGKKQLGEAFTPGS---HGTTFGGNMLAMAAVNATLQIVFQPDFLQEAADKGAFLK 301
           VGA  GK+++ +   P        T  GN LAMAA  ATL ++ + D+    A   AF+K
Sbjct: 274 VGAYGGKREIMQRIAPCGEVYQAGTLSGNPLAMAAGIATLDVLSRSDYAGLEARVAAFVK 333

Query: 302 EQLEAELK 309
           E LEA LK
Sbjct: 334 E-LEAILK 340


Lambda     K      H
   0.318    0.135    0.390 

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: 378
Number of extensions: 17
Number of successful extensions: 5
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: 385
Length of database: 423
Length adjustment: 31
Effective length of query: 354
Effective length of database: 392
Effective search space:   138768
Effective search space used:   138768
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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