GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Phyllobacterium brassicacearum STM 196

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_106713043.1 CU102_RS20965 acetylornithine deacetylase

Query= curated2:Q5FPX5
         (381 letters)



>NCBI__GCF_003010955.1:WP_106713043.1
          Length = 374

 Score = 91.7 bits (226), Expect = 3e-23
 Identities = 76/209 (36%), Positives = 102/209 (48%), Gaps = 27/209 (12%)

Query: 69  PALCFAGHTDVVPPGE-GWAHDPFAAVIEGDRLYGRGIADMKGGVACFVAAVARRLEQGP 127
           P    +GH DVVP GE GW  DPF    +G RL GRG  DMKG +AC +AA+  +L    
Sbjct: 62  PGYILSGHLDVVPAGEAGWKTDPFQLQRDGKRLCGRGTTDMKGFLACALAALP-KLAASN 120

Query: 128 LKGSVSLLITGDEEGPAHFGTKPVIEWLAERGELPDFC------VLGEPTNPQALGDVIK 181
           L+  V L  + DEE     G + V   LA    LPD C      ++GEP+  QA+     
Sbjct: 121 LQRPVHLAFSYDEEA----GCRGVPHLLA---ALPDLCAKPLGAIIGEPSRMQAVR---- 169

Query: 182 IGRRGSMNAVVTVHGTQGHVAYPHLADNPVHRL--LAAFSELTARELDAG--SEWFDP-- 235
              +G   A + V G  GH + P L  N VH +  + A + +  R L+ G   + F+P  
Sbjct: 170 -AHKGKAAARLEVAGRSGHSSRPDLGLNAVHAMANVIAQAVVYGRSLEQGPFDDNFEPPY 228

Query: 236 SSLQVTSIDVGNGATNIIPGSAVGRLNIR 264
           SSLQ   +  G  A NIIP      + +R
Sbjct: 229 SSLQFGVVS-GGQAVNIIPDRCTADIEVR 256


Lambda     K      H
   0.319    0.138    0.422 

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: 413
Number of extensions: 29
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: 381
Length of database: 374
Length adjustment: 30
Effective length of query: 351
Effective length of database: 344
Effective search space:   120744
Effective search space used:   120744
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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