GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Burkholderia phytofirmans PsJN

Align shikimate dehydrogenase (EC 1.1.1.25); quinate/shikimate dehydrogenase (EC 1.1.1.282) (characterized)
to candidate BPHYT_RS22685 BPHYT_RS22685 shikimate 5-dehydrogenase

Query= BRENDA::Q88K85
         (282 letters)



>FitnessBrowser__BFirm:BPHYT_RS22685
          Length = 304

 Score =  334 bits (857), Expect = 1e-96
 Identities = 168/274 (61%), Positives = 203/274 (74%)

Query: 7   LAGLIGRGIQLSRTPALHEHEGDAQALRYLYRLIDADQLQLDDSALPGLLEAAQHTGFTG 66
           L GLIG GI  S TPA+HE EG    L Y+YR ID + L+LD +ALP LL AA+  GF G
Sbjct: 27  LVGLIGAGIGGSLTPAMHEEEGSKLGLHYVYRRIDLEALKLDVAALPDLLMAAERMGFNG 86

Query: 67  LNITYPFKQAILPLLDELSDEARGIGAVNTVVLKDGKRVGHNTDCLGFAEGLRRGLPDVA 126
           LNITYP KQA++PLLDELSD+AR +GAVNTV+ KDG+R+GHNTD  GFA   +RGLPDV+
Sbjct: 87  LNITYPCKQAVIPLLDELSDDARALGAVNTVLFKDGRRIGHNTDWSGFARAFQRGLPDVS 146

Query: 127 RRQVVQMGAGGAGSAVAHALLGEGVERLVLFEVDATRAQALVDNLNTHFGAERAVLGTDL 186
             +VVQ+GAGGAG+AVAHA L  G + L LF+VDATRA +L D L   F A     G+ L
Sbjct: 147 LERVVQLGAGGAGAAVAHAALNMGAKSLTLFDVDATRAASLADELQKRFPAAAVGAGSSL 206

Query: 187 ATALAEADGLVNTTPVGMAKLPGTPLPVELLHPRLWVAEIIYFPLETELLRAARALGCRT 246
           A +LA A+GL++ TP GMAKLPG PLPVELLH  LWVA+I+YFP+ T LL+AA ALGCRT
Sbjct: 207 AESLAAANGLIHATPTGMAKLPGLPLPVELLHRDLWVADIVYFPIRTALLQAAEALGCRT 266

Query: 247 LDGSNMAVFQAVKAFELFSGRQADAARMQAHFAS 280
           L G  MAV+QAV A  +F+G + DA R+  HF S
Sbjct: 267 LSGGGMAVYQAVDAMRIFTGLEPDAERVYTHFQS 300


Lambda     K      H
   0.321    0.137    0.395 

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: 240
Number of extensions: 7
Number of successful extensions: 1
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: 282
Length of database: 304
Length adjustment: 26
Effective length of query: 256
Effective length of database: 278
Effective search space:    71168
Effective search space used:    71168
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 (21.9 bits)
S2: 48 (23.1 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