GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydratase in Pseudomonas fluorescens GW456-L13

Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate PfGW456L13_3978 Cyclohexadienyl dehydratase (EC 4.2.1.51)(EC 4.2.1.91)

Query= BRENDA::Q01269
         (268 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3978
          Length = 254

 Score =  242 bits (618), Expect = 5e-69
 Identities = 122/243 (50%), Positives = 168/243 (69%), Gaps = 2/243 (0%)

Query: 17  LLASASLQAQESRLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDMAQRLAESLGA 76
           L  S   QA+ S LD +++ G LRV TTGDYKP++ + E+G Y+G D+ MA+ LA+SLG 
Sbjct: 7   LALSLGAQAEPSHLDSVMQQGQLRVCTTGDYKPYTLKAEDGEYSGIDIAMARALADSLGV 66

Query: 77  KLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPITLCSEEAR 136
           K+  VPT+W  LM D    + DIAM GIS+ LERQ++A+FS     DGK P+  C ++A 
Sbjct: 67  KVEWVPTTWKTLMPDMLAGKCDIAMGGISVTLERQKKAFFSSILDVDGKIPLVRCEDQAL 126

Query: 137 FQTLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQIVDGKADLMMTDA 196
           +QT+EQI++P V  +   GGTNE F  A L KA++ +H DNVTIFQ+++D KAD+M+TDA
Sbjct: 127 YQTVEQINRPTVRLVEPAGGTNEAFVHAFLPKAQLKLH-DNVTIFQELLDKKADVMITDA 185

Query: 197 IEARLQSRLHPELCAVHPQQPFDFAEKAYLLPRDE-AFKRYVDQWLHIAEQSGLLRQRME 255
            EA  Q +L P LCAV+P     + EKAYLLPRD+  +K YVDQWLH+A+ +G  ++ + 
Sbjct: 186 SEALYQQKLKPGLCAVNPTHYMQYGEKAYLLPRDDITWKLYVDQWLHLAKATGNYQKILR 245

Query: 256 HWL 258
            WL
Sbjct: 246 QWL 248


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: 205
Number of extensions: 8
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: 254
Length adjustment: 25
Effective length of query: 243
Effective length of database: 229
Effective search space:    55647
Effective search space used:    55647
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