GapMind for Amino acid biosynthesis

 

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

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate Ac3H11_1332 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= reanno::azobra:AZOBR_RS19025
         (389 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1332
          Length = 398

 Score =  322 bits (826), Expect = 9e-93
 Identities = 173/389 (44%), Positives = 238/389 (61%), Gaps = 4/389 (1%)

Query: 3   PVVMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKL 62
           P VM TY R  I  ERG+G  ++  +G+ ++D   G+AVN LGH +  LV AL  Q  KL
Sbjct: 10  PHVMNTYGRVPIALERGQGCRVWDVNGKEYIDGLGGIAVNTLGHNHGKLVPALQDQIAKL 69

Query: 63  WHTSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRI 122
            HTSN + V  QE LA +L E +    VFF NSG EA E   K+ RK+  +KG  A+  I
Sbjct: 70  IHTSNYYHVPLQEKLATKLVELSGMQNVFFCNSGLEANEAALKIARKFGVDKGI-AKPEI 128

Query: 123 ITFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAV--TDETAGICL 180
           + +E+AFHGR++A +SA    K+  GFGPL++GF  VP  D+EA++ A         +  
Sbjct: 129 VVYEKAFHGRSIATMSATGNPKIHNGFGPLVEGFVRVPMNDIEAIKQATEGNPNVVAVFF 188

Query: 181 EPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMA 240
           E IQGEGGI    +E+L+ LR++CDE G L+ +DE+QCGMGRTGK FAH+WAGI PDVM 
Sbjct: 189 ETIQGEGGINGMRIEYLQQLRKLCDERGWLMMIDEVQCGMGRTGKWFAHQWAGIVPDVMP 248

Query: 241 VAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQ 300
           +AKG+G G P+GA +A  KAA+ +  G HG+T+GGNPLA   G   +  + E G L +  
Sbjct: 249 LAKGLGSGVPIGAVVAGPKAANVLQPGNHGTTFGGNPLAMRAGVETIRIMEEDGLLHNAA 308

Query: 301 RIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNV 360
           ++G  L+  L   +   P V K +RG+GLMLG+      G ++      GLL     D+V
Sbjct: 309 QVGDHLRAALQRELGSLPGV-KEIRGQGLMLGIELNKPCGALIGRAAEAGLLLSVTADSV 367

Query: 361 VRLLPPLNIGEAEVEEAVAILAKTAKELV 389
           +RL+PPL +  AE +  VAIL    K ++
Sbjct: 368 IRLVPPLILTTAEADAIVAILTPLVKAIL 396


Lambda     K      H
   0.321    0.139    0.414 

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: 496
Number of extensions: 24
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: 389
Length of database: 398
Length adjustment: 31
Effective length of query: 358
Effective length of database: 367
Effective search space:   131386
Effective search space used:   131386
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