GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cmutase in Magnetospirillum magneticum AMB-1

Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_011386516.1 AMB_RS21090 prephenate dehydratase

Query= CharProtDB::CH_024084
         (386 letters)



>lcl|NCBI__GCF_000009985.1:WP_011386516.1 AMB_RS21090 prephenate
           dehydratase
          Length = 289

 Score =  150 bits (379), Expect = 4e-41
 Identities = 99/277 (35%), Positives = 140/277 (50%), Gaps = 6/277 (2%)

Query: 100 NPHSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIE 159
           NP  A IAF G  G+YSHLA R      +       CA F D F  V  G+A YA++PI+
Sbjct: 6   NPDQA-IAFQGEPGAYSHLACRNA----YPGMQPLPCATFEDTFAAVREGRARYAMIPID 60

Query: 160 NTSSGAINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKF 219
           N+ +G + DV+ L+ +  L I+ E    I H LLV     L TI TV SH     QC   
Sbjct: 61  NSVAGRVADVHHLMPYAGLHIIAEHFERISHHLLVVPGATLDTIKTVKSHVHALGQCRNL 120

Query: 220 LNRYPHWKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTR 279
           +       I  T++  AA E +A+ + P +AA+ SE     YGL  L+    +   N TR
Sbjct: 121 IRELGLKVIVGTDTAGAAAE-LAERQDPTMAAIASELAAEAYGLVSLKAGIEDAEHNTTR 179

Query: 280 FVVLARKAINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWE 339
           FVVLAR+A+  +   P  TT +      A AL +AL     + + MTRLES  + G    
Sbjct: 180 FVVLAREALEPNPNQPCVTTFVFRVRNVAAALYKALGGFATNGINMTRLESYMVGGEFAA 239

Query: 340 EMFYLDIQANLESAEMQKALKELGEITRSMKVLGCYP 376
             FY D++ +     ++ AL+EL   +  +++LG YP
Sbjct: 240 TQFYADVEGHPTQRNLRLALEELDFFSHEVRILGVYP 276


Lambda     K      H
   0.318    0.132    0.374 

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: 238
Number of extensions: 13
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: 386
Length of database: 289
Length adjustment: 28
Effective length of query: 358
Effective length of database: 261
Effective search space:    93438
Effective search space used:    93438
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 (21.8 bits)
S2: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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