GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Cup4G11:RR42_RS18295
          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 (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