GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cmutase in Cupriavidus basilensis 4G11

Align Salicylate synthase; Chorismate mutase; CM; EC 5.4.99.5; Isochorismate synthase/isochorismate lyase; EC 4.2.99.21; EC 5.4.4.2; Mycobactin synthase protein (uncharacterized)
to candidate RR42_RS18295 RR42_RS18295 anthranilate synthase component I

Query= curated2:Q73XV3
         (450 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS18295 RR42_RS18295 anthranilate
           synthase component I
          Length = 505

 Score =  142 bits (359), Expect = 2e-38
 Identities = 90/264 (34%), Positives = 130/264 (49%), Gaps = 11/264 (4%)

Query: 183 DPSNYRDRVASAVAEIAAGRYHKVILSRCLQVPFAVDFPSTYRLARRHNTPVRSFLLRLG 242
           + ++Y   V  A   I AG   +V + + L  P+     + YR  R  N     +    G
Sbjct: 220 EKADYLAAVHKAKEYIMAGDMMQVQIGQRLVKPYRDSPLTLYRALRSLNPSPYMYFYNFG 279

Query: 243 GIRAVGYSPELVAAV-----------RHDGVVVTEPLAGTRAFGRGALHDRQARDDLESN 291
             + VG SPE++              R D +V   PLAGTRA G     D Q   +L ++
Sbjct: 280 DFQIVGASPEILVRQETRRVGSNGDQREDHIVTIRPLAGTRARGNTPEKDAQLATELLND 339

Query: 292 SKEIVEHAISVRSSLQEMAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRLGTSNDRMD 351
            KEI EH + +  +  ++  IAE G+  VTD M + +   VQH+ S+V G L      +D
Sbjct: 340 PKEIAEHVMLIDLARNDIGRIAEIGSVKVTDQMVIEKYSHVQHIVSSVEGTLKPGMSNLD 399

Query: 352 ALEALFPAVTASGIPKAGGVEAILRLDEGPRGLYSGAVVMVSADGALDAALTLRAAYEHD 411
            L A FPA T SG PK   +E I  L+   RG+Y GAV  +S  G +D A+ +R     D
Sbjct: 400 VLRATFPAGTLSGAPKVHAMEIIDELEPRKRGIYGGAVGYLSFGGEMDLAIAIRTGIVKD 459

Query: 412 GKTWLRAGAGIIEESTPEREFEET 435
           G  +++A AGI+ +S PE E+ ET
Sbjct: 460 GNLYVQAAAGIVADSDPEAEWRET 483


Lambda     K      H
   0.318    0.135    0.391 

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: 447
Number of extensions: 19
Number of successful extensions: 2
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: 450
Length of database: 505
Length adjustment: 33
Effective length of query: 417
Effective length of database: 472
Effective search space:   196824
Effective search space used:   196824
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: 51 (24.3 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 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