GapMind for Amino acid biosynthesis

 

Aligments for a candidate for pre-dehydr in Shewanella amazonensis SB2B

Align prephenate dehydrogenase (EC 1.3.1.12); prephenate dehydratase (EC 4.2.1.51); Chorismate mutase (EC 5.4.99.5) (characterized)
to candidate 6936711 Sama_0898 prephenate dehydratase / chorismate mutase / phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= BRENDA::O30012
         (620 letters)



>lcl|FitnessBrowser__SB2B:6936711 Sama_0898 prephenate dehydratase /
           chorismate mutase / phospho-2-dehydro-3-deoxyheptonate
           aldolase (RefSeq)
          Length = 659

 Score =  162 bits (411), Expect = 3e-44
 Identities = 114/378 (30%), Positives = 198/378 (52%), Gaps = 30/378 (7%)

Query: 261 KKAESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMS 320
           +K + + E R  I  ID+ +L+L+ RR + + ++AR K     P+     E E L  ++ 
Sbjct: 2   EKPQPLSETREQITDIDNTVLQLLARRRELSLEVARSKEVDVRPVRDTQRERELLSRLVQ 61

Query: 321 KTT---LNPVKLKEIFEGIM--SLAKEEEY-------KVAGVKYTIAVLGPQGSFSEEMA 368
           K     L+P  + ++++ I+  S+  ++ Y       +    +Y IA LG +GS+S   A
Sbjct: 62  KGREQGLDPHFVMQLYQSIIEDSVLNQQAYLHGRANPETQKQQYCIAYLGARGSYSYLAA 121

Query: 369 LKLVGSR----VPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVE 424
            +    R    V L  C + DEI+  VESG  DYG +PIEN+ +G++  V D L +  + 
Sbjct: 122 NRYCQRRQVDMVDLG-CQSFDEIVHAVESGHADYGFLPIENTSSGSINEVYDVLQHTSLA 180

Query: 425 VFGEAKLEVNHCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAA 484
           + GE  +EV HCL+AK   +  +IKT+Y+HPQ ++QC  ++  + P + + Y  S+++A 
Sbjct: 181 IVGETTIEVGHCLLAKPGTKASDIKTLYAHPQPISQCSRYLARH-PGLRLEYCASSAEAM 239

Query: 485 RMLDDYS----AAIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGKI--- 537
             +        AAI S      Y+L  + KG+ + K  N +RF ++ R++     ++   
Sbjct: 240 EKVQAADSKDVAAIGSAEGGGLYQLEAIEKGLANQK-VNQSRFIVVARKAVAVPEQLPAK 298

Query: 538 TSLFFGVEDKPGALKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPL----REE 593
            +L      KPGAL + L V      N+ KLESRP      + +F+++++A L     + 
Sbjct: 299 CTLIMATGQKPGALVEALLVLKANNLNMSKLESRPIPGTPWEEMFYLDIDANLASVPMQL 358

Query: 594 DLLDLKQVTTFYKVVGVF 611
            L +L+++T F KV+G +
Sbjct: 359 ALKELERITRFIKVLGCY 376


Lambda     K      H
   0.320    0.137    0.380 

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: 698
Number of extensions: 33
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: 620
Length of database: 659
Length adjustment: 38
Effective length of query: 582
Effective length of database: 621
Effective search space:   361422
Effective search space used:   361422
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 (21.8 bits)
S2: 54 (25.4 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