GapMind for Amino acid biosynthesis

 

Aligments for a candidate for pre-dehydr in Dechlorosoma suillum PS

Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate Dsui_1941 Dsui_1941 prephenate dehydrogenase

Query= uniprot:D8IR44_HERSS
         (295 letters)



>lcl|FitnessBrowser__PS:Dsui_1941 Dsui_1941 prephenate dehydrogenase
          Length = 290

 Score =  327 bits (837), Expect = 3e-94
 Identities = 165/283 (58%), Positives = 206/283 (72%)

Query: 2   FKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAVQ 61
           F KVVIFGVGLIGGSFAL LR AG    +VG GRS +SL++A +LG+ID    + A  + 
Sbjct: 4   FNKVVIFGVGLIGGSFALGLRAAGAVEEVVGFGRSPKSLQQALDLGVIDRAGINPAHELS 63

Query: 62  GADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPAH 121
            ADL+L+A PV Q   I+A I P+L P+ +VTD GSTK DVVAAAR A G+RI QF+PAH
Sbjct: 64  DADLVLLATPVGQMPEIMARIVPYLGPETVVTDGGSTKGDVVAAARAAFGERIGQFVPAH 123

Query: 122 PIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHDA 181
           PIAG E  G  AA A+LY  +KVV+T LPEN   +V  V +AW  CGA I+ L+P EHD 
Sbjct: 124 PIAGAENSGAAAARADLYRERKVVLTPLPENSVLNVAKVRSAWEWCGAQIYELTPAEHDR 183

Query: 182 VFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANRD 241
           VFA+VSHLPH+L+FALV D+A + +    F +AASGFRDFTRIAAS PEMWRDI LAN+D
Sbjct: 184 VFAAVSHLPHLLSFALVHDLAVRENKELFFTFAASGFRDFTRIAASHPEMWRDICLANKD 243

Query: 242 ALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQWA 284
           ALL E+D+Y  QL  +   +AAGDG  +E+I+ +A+ AR+ WA
Sbjct: 244 ALLLELDSYRAQLDELHQALAAGDGRRLEEIFDTARTARRDWA 286


Lambda     K      H
   0.320    0.132    0.376 

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: 273
Number of extensions: 12
Number of successful extensions: 1
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: 295
Length of database: 290
Length adjustment: 26
Effective length of query: 269
Effective length of database: 264
Effective search space:    71016
Effective search space used:    71016
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: 48 (23.1 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