GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Pseudomonas fluorescens FW300-N2E2

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate Pf6N2E2_3203 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)

Query= BRENDA::A9CFV4
         (303 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3203
          Length = 295

 Score =  147 bits (371), Expect = 3e-40
 Identities = 98/288 (34%), Positives = 148/288 (51%), Gaps = 4/288 (1%)

Query: 5   GIYTPAITPLGHDGE-IDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDLAAY 63
           GI    ITP   DG+ +D DA    ++ L+++ VH I   GSTGE    +  E   ++ +
Sbjct: 8   GIIGYTITPFSTDGQGLDLDALGRSIDRLIDSGVHAIAPLGSTGEGAYLSDAEWDQVSEF 67

Query: 64  ARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHALAV 123
           +   +  R+P VV      T  ++  A+ A+  GAD ++V    Y   +E E   H  A+
Sbjct: 68  SIARVAGRVPTVVSVSDLTTAKAVHRARFAQAKGADVVMVLPASYWKLSEAEILAHYQAI 127

Query: 124 DRAANLPIMLYNYPARMGVVMGEEYFSRVGKS-KNVVAIKESSGDMGNLHLLARKFP-QI 181
             + +LPIMLYN PA  G+ M  E   R+  +  NV  +KES+GD+  +H L      Q+
Sbjct: 128 GASIDLPIMLYNNPATSGIDMSVELILRIFNTVDNVTMVKESTGDIQRMHKLQLLGEGQV 187

Query: 182 ALSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLPLM 241
               G +  ALE FA GAK W  A  N +P+ ++ LY A V+  +  + RA+    LPL+
Sbjct: 188 PFYNGCNPLALEAFAAGAKGWCTAAPNLIPQLNLDLY-AAVLANDLSQARALFYRQLPLL 246

Query: 242 DFLECGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQTVVTTL 289
           DF+  G    +IK G   +GL  G  R P+ PL+    + LQT++  L
Sbjct: 247 DFILKGGLPATIKAGLRTLGLEVGDPRLPVFPLDEARNQQLQTMLKQL 294


Lambda     K      H
   0.320    0.135    0.397 

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: 195
Number of extensions: 11
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: 303
Length of database: 295
Length adjustment: 27
Effective length of query: 276
Effective length of database: 268
Effective search space:    73968
Effective search space used:    73968
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: 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