GapMind for Amino acid biosynthesis

 

Alignments for a candidate for pre-dehydr in Salinicoccus carnicancri Crm

Align Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 (characterized)
to candidate WP_017547588.1 C792_RS0101060 prephenate dehydrogenase

Query= SwissProt::Q04983
         (293 letters)



>NCBI__GCF_000330705.1:WP_017547588.1
          Length = 287

 Score =  113 bits (283), Expect = 4e-30
 Identities = 83/275 (30%), Positives = 128/275 (46%), Gaps = 7/275 (2%)

Query: 7   IAIIGLGLIGSSAARATKAYCPDVTVSLYDKSEFVRDRARALNLGDNVTDDIQDAVREAD 66
           I I GLG IG S A A K+  P+  V   D        A    L     +  +  +  AD
Sbjct: 3   IVIAGLGNIGGSFALAIKSNAPEHEVYAIDIDAESLRNAEDSGLIKKGYETPESIIPHAD 62

Query: 67  LVLLCVPVRAMGIVAAAMAPALKKDVIICDTGSVKVSVIKTLQDNLPNHI-IVPSHPLAG 125
           LV+  V    +  + A  AP  K++VI+ D   VK S+I+ ++  L ++   V  HP+AG
Sbjct: 63  LVIFSVYPMILKSLVAEYAPYFKENVILTDVTGVKRSIIEEIEPLLSDNADFVFGHPMAG 122

Query: 126 TENNGPDAGFAELFQDHPVILTPDAHTPAQAIAYIADYWEEIGGR-INLMSAEHHDHVLA 184
            EN G      E+F+    + TP      + I  ++ +  EIG R +  ++ + HD V+ 
Sbjct: 123 RENRGLSFASGEVFRGANYLFTPTPGNKPENIEMLSSFVREIGFRNVTSITPDFHDEVIG 182

Query: 185 LTSHLPHVIAYQLIGMVSGYEKKSRTPIMRYSAGSFRDATRVAASEPRLWQDIMLENAPA 244
            TS L HVIA  LI         +      Y+  S+RD TR+     +LW ++ + N   
Sbjct: 183 FTSQLAHVIAVSLIN-----SDDTNRDTKAYTGDSYRDLTRITNINEKLWPELFIMNKDH 237

Query: 245 LLPVLDHFIADLKKLRTAIASQDGDYLLEHFKESQ 279
           LL  +D F   L +L  AI ++D + + E   ES+
Sbjct: 238 LLNHIDGFKEQLDQLTKAIENEDVETMQEMMIESR 272


Lambda     K      H
   0.321    0.136    0.398 

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: 201
Number of extensions: 13
Number of successful extensions: 5
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: 293
Length of database: 287
Length adjustment: 26
Effective length of query: 267
Effective length of database: 261
Effective search space:    69687
Effective search space used:    69687
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: 48 (23.1 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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