GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Pseudomonas fluorescens GW456-L13

Align diaminopimelate epimerase (EC 5.1.1.7) (characterized)
to candidate PfGW456L13_2444 Diaminopimelate epimerase (EC 5.1.1.7)

Query= BRENDA::E4NI20
         (295 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2444
          Length = 330

 Score = 70.1 bits (170), Expect = 6e-17
 Identities = 82/260 (31%), Positives = 113/260 (43%), Gaps = 70/260 (26%)

Query: 84  NADGSIAEMCGNGVRVFARYLVHAGHAGSGELAVATRGGVKRVRIAADAPDG-TPGDVTV 142
           N DG++AE  GNG+ +F++ L   G     E  +        +R+  D  D  +PG  +V
Sbjct: 86  NTDGTLAERSGNGLTIFSQALSDQGLLPQNEACL--------LRVHHDKADSPSPGQTSV 137

Query: 143 -------------DMGRAAFPGPD-----GVTVTV-DGRSWP------ALN--------V 169
                        D+G+  F GP      GV  T+ +GR         ALN         
Sbjct: 138 KAAEVGGVKGFWLDLGQPGF-GPSAVSAHGVEATIFNGRELSHVEQLSALNSAWSHSQFA 196

Query: 170 NMGNPHAVAFVE---DLAHAGHLYEAPATA----------PAGA---YPQGVNVEFVVDR 213
            +GNPH V  VE   DL     + E PA            P GA    P G+N+++ +  
Sbjct: 197 RVGNPHCVTLVESAEDLPSNEQMRE-PALGEGLTRIAYAMPVGAGKPCPAGINLQWAMRV 255

Query: 214 GERHVAMRVHERGSGETRSCGTGACAVAVAAIRRDGADPAATGEAVRYTVDVPGGR---L 270
            E H+A RV ERG G T S GT A AVA AA R   A   + GE     V +PGG    L
Sbjct: 256 SEGHIAARVFERGEGPTASSGTSASAVACAAWR---AGWVSAGEV---KVTMPGGTAPIL 309

Query: 271 VIEEFPD-GRIEMTGPAVIV 289
           + EE  +  R+ + G A ++
Sbjct: 310 LAEELGELSRVSLFGTARLI 329


Lambda     K      H
   0.318    0.135    0.408 

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: 303
Number of extensions: 19
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: 295
Length of database: 330
Length adjustment: 27
Effective length of query: 268
Effective length of database: 303
Effective search space:    81204
Effective search space used:    81204
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: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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