GapMind for Amino acid biosynthesis

 

Alignments for a candidate for preph-dehydratase in Pseudomonas fluorescens FW300-N2E2

Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate Pf6N2E2_1300 Cyclohexadienyl dehydratase (EC 4.2.1.51)(EC 4.2.1.91)

Query= BRENDA::Q01269
         (268 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1300
          Length = 263

 Score =  238 bits (608), Expect = 7e-68
 Identities = 122/245 (49%), Positives = 165/245 (67%), Gaps = 2/245 (0%)

Query: 15  LALLASASLQAQESRLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDMAQRLAESL 74
           LAL   A  +   S LD++L+ G L+V TTGDYKP++++T  G Y G D+DMA+ LA SL
Sbjct: 14  LALSCGALAEPTPSLLDQVLQRGELKVCTTGDYKPYTFKTATGEYEGIDIDMARSLAASL 73

Query: 75  GAKLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPITLCSEE 134
           G K+  V T+W  LM D    + DI M GIS+ LERQ++AYFS     DGK P+  C ++
Sbjct: 74  GVKVQWVQTTWKTLMPDMVAGQCDIGMGGISVTLERQKKAYFSDTLDVDGKIPLVRCEDK 133

Query: 135 ARFQTLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQIVDGKADLMMT 194
            R+QTLEQ++QP V  +   GGTNE F RA L   ++  H DNVTIFQQ++D KAD+M+T
Sbjct: 134 ERYQTLEQMNQPSVRLVEPAGGTNEAFVRAFLPNGQLNFH-DNVTIFQQLLDKKADVMIT 192

Query: 195 DAIEARLQSRLHPELCAVHPQQPFDFAEKAYLLPRDE-AFKRYVDQWLHIAEQSGLLRQR 253
           DA EA  Q +L P LCAV+P +   + EKAYLLPRD+  +K YVDQWLH+++ +G  ++ 
Sbjct: 193 DASEALYQQKLKPGLCAVNPTRYLQYGEKAYLLPRDDNTWKMYVDQWLHLSKANGSYQKV 252

Query: 254 MEHWL 258
           +  WL
Sbjct: 253 IGQWL 257


Lambda     K      H
   0.322    0.135    0.406 

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: 203
Number of extensions: 9
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: 268
Length of database: 263
Length adjustment: 25
Effective length of query: 243
Effective length of database: 238
Effective search space:    57834
Effective search space used:    57834
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: 47 (22.7 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