GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Dyella japonica UNC79MFTsu3.2

Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (characterized)
to candidate N515DRAFT_4364 N515DRAFT_4364 homoserine dehydrogenase

Query= SwissProt::P31116
         (359 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4364
          Length = 362

 Score =  198 bits (504), Expect = 2e-55
 Identities = 133/352 (37%), Positives = 199/352 (56%), Gaps = 18/352 (5%)

Query: 8   VAVIGAGVVGSAFLDQLLAMKSTITYNLVLLAEAERSLISKDFSPLNVGSDWKAALAAST 67
           + + G GVVG A L +LL   +  +  LV  A + R   S +       +D +A      
Sbjct: 24  IVLFGTGVVGGALL-KLLNTPAAASLRLVGAANSRRQQTSAEQL-----AD-RALREKLK 76

Query: 68  TKTLPLDD--LIAHLKTSPKPV-ILVDNTSSAYIAGFYTKFVENGISIATPNKKAFSSDL 124
           +   P DD  L+  L TS   V +++D T++A +A  +  ++  G  + T NK     +L
Sbjct: 77  SHGDPRDDATLLRALDTSGAAVKVIIDATANANLAARHADWLARGYHVVTANKALAGGEL 136

Query: 125 ATWKALFSNKPTNGFVYHEATVGAGLPIISFLREIIQTGDEVEKIEGIFSGTLSYIFNEF 184
             W+AL +     G     ATVGAGLP++S LR +   GD +  +EG+FSG+LSY+FN++
Sbjct: 137 PGWRALQAAVAQGGRYGDAATVGAGLPVLSTLRRLRACGDALLTLEGVFSGSLSYLFNQY 196

Query: 185 STSQANDVKFSDVVKVAKKLGYTEPDPRDDLNGLDVARKVTIVGRISGVEVESPTSFPVQ 244
             SQ     FS +++ A+KLGYTEPDPR DL+G DVARK+ I+ R +G  +       V+
Sbjct: 197 DGSQ----PFSGLLREARKLGYTEPDPRSDLSGEDVARKLLIIARNAGFAL-GTDEVEVE 251

Query: 245 SLIPKPLESVKSADEFLEKLSDYDKDLTQLKKEAATENKVLRFIGKVDVATKSVSVGIEK 304
           SL+P+ L SV   D FL +L + D+ L +   EA     VLRF+ +++   K+  VG+ +
Sbjct: 252 SLVPEALRSV-DTDSFLARLEELDEPLARRHAEAKARGGVLRFLARLNQRGKA-RVGLVE 309

Query: 305 YDYSHPFASLKGSDNVISIKTKRY-TNPVVIQGAGAGAAVTAAGVLGDVIKI 355
              +HP A L G+DN  ++ T RY + P+VIQG GAG  VTA  +LGDV+ +
Sbjct: 310 VPATHPAARLYGTDNQFALTTTRYHSQPLVIQGPGAGPEVTAQALLGDVLAL 361


Lambda     K      H
   0.314    0.132    0.361 

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: 205
Number of extensions: 9
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: 359
Length of database: 362
Length adjustment: 29
Effective length of query: 330
Effective length of database: 333
Effective search space:   109890
Effective search space used:   109890
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: 42 (22.0 bits)
S2: 49 (23.5 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