GapMind for Amino acid biosynthesis

 

Aligments for a candidate for pre-dehydr in Shewanella sp. ANA-3

Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate 7025863 Shewana3_3012 bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq)

Query= ecocyc::CHORISMUTPREPHENDEHYDROG-MONOMER
         (373 letters)



>lcl|FitnessBrowser__ANA3:7025863 Shewana3_3012 bifunctional
           chorismate mutase/prephenate dehydrogenase (RefSeq)
          Length = 379

 Score =  423 bits (1088), Expect = e-123
 Identities = 212/368 (57%), Positives = 270/368 (73%), Gaps = 1/368 (0%)

Query: 4   ELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAEAEA 63
           EL  LR  ID VD+ LL+LL KRL+LVA+VG VK   GLPIY P+REA+MLA RR EA+ 
Sbjct: 8   ELEHLRGLIDGVDQQLLHLLRKRLDLVAQVGTVKHAAGLPIYAPQREAAMLAKRREEAKT 67

Query: 64  LGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTLSGY 123
           +G+ P LIED+LRR+MRESY +E D GFK +   L  VVIVGG GQ+G LF++ML+LSGY
Sbjct: 68  MGIAPQLIEDILRRLMRESYLNEKDVGFKQVKNDLGSVVIVGGKGQLGGLFQQMLSLSGY 127

Query: 124 QVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIG-KLPPLPKDCILVDLASVKNGPL 182
           QV++L++ DW +A  + ADAG+V+V+VPI +T  +I  KL  LP++CIL DL S+K  P+
Sbjct: 128 QVKVLDKDDWQQAETLFADAGLVLVTVPIAITCDIIREKLTQLPQECILADLTSIKTEPM 187

Query: 183 QAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRISA 242
            AML AH GPV+G HPMFGPD GSLAKQVVV C GR  + YQW LEQI +WGAR+     
Sbjct: 188 NAMLAAHKGPVVGFHPMFGPDVGSLAKQVVVVCHGRGADKYQWLLEQIGIWGARIVEAEP 247

Query: 243 VEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDPQL 302
             HD  M  +QA+RHF+TF YGL+L +E   +E LL  SSPIYRLELAMVGRLFAQ P+L
Sbjct: 248 ERHDNAMQLVQAMRHFSTFVYGLNLCKEEADIETLLQFSSPIYRLELAMVGRLFAQSPEL 307

Query: 303 YADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSESR 362
           YADII + + +   I  Y   + EA+ELL++GD+ AFI  F+ V  WFGD+A +FQ ESR
Sbjct: 308 YADIIFAQQDSQHAIGDYLDNYREALELLKRGDRDAFISQFQTVAKWFGDFAPQFQRESR 367

Query: 363 VLLRQAND 370
           ++L+  +D
Sbjct: 368 MMLQSVSD 375


Lambda     K      H
   0.322    0.138    0.404 

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: 390
Number of extensions: 14
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: 373
Length of database: 379
Length adjustment: 30
Effective length of query: 343
Effective length of database: 349
Effective search space:   119707
Effective search space used:   119707
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 (21.9 bits)
S2: 50 (23.9 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