GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydr in Phaeobacter inhibens BS107

Align Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 (characterized)
to candidate GFF2491 PGA1_c25230 protein TyrC

Query= SwissProt::Q04983
         (293 letters)



>FitnessBrowser__Phaeo:GFF2491
          Length = 306

 Score =  229 bits (585), Expect = 4e-65
 Identities = 117/281 (41%), Positives = 176/281 (62%), Gaps = 1/281 (0%)

Query: 3   VFKHIAIIGLGLIGSSAARATKAYCPDVTVSLYDKSEFVRDRARALNLGDNVTDDIQDAV 62
           ++  IA+IGLGLI SS A A +       ++ Y +S   RD AR +NL D V D   +A 
Sbjct: 5   IYNRIALIGLGLIASSMAHAIRRGGLASEITGYARSAETRDTARRINLCDRVCDTAAEAA 64

Query: 63  READLVLLCVPVRAMGIVAAAMAPALKKDVIICDTGSVKVSVIKTLQDNLPNHI-IVPSH 121
           ++ADL++LCVPV AM  V A +AP LK    + D GSVK  VI  +Q ++P  +  VP+H
Sbjct: 65  QDADLIVLCVPVGAMDAVMADIAPVLKPGATVSDVGSVKRHVIDAVQPHIPEGVHFVPAH 124

Query: 122 PLAGTENNGPDAGFAELFQDHPVILTPDAHTPAQAIAYIADYWEEIGGRINLMSAEHHDH 181
           PLAGTE++GP+AGFAEL+ +   +L P   +    +  +   WE +G  ++ M A+HHD 
Sbjct: 125 PLAGTEHSGPEAGFAELYDNRWCLLVPVEGSDRAPVDRLRQLWEGMGANVDEMDADHHDL 184

Query: 182 VLALTSHLPHVIAYQLIGMVSGYEKKSRTPIMRYSAGSFRDATRVAASEPRLWQDIMLEN 241
           VLA+TSH PH+IAY ++G+     + + + +++YSA  FRD TR+AAS+P +W+D+ L N
Sbjct: 185 VLAVTSHAPHLIAYTMVGVADDLRRVTDSEVIKYSAAGFRDFTRIAASDPTMWRDVFLTN 244

Query: 242 APALLPVLDHFIADLKKLRTAIASQDGDYLLEHFKESQKAR 282
             A L +L  F  +L  L+ AI + DG++L ++F  ++  R
Sbjct: 245 KDATLEILGRFTEELFALQRAIRTGDGEHLHQYFTRTRAIR 285


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: 261
Number of extensions: 12
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: 293
Length of database: 306
Length adjustment: 27
Effective length of query: 266
Effective length of database: 279
Effective search space:    74214
Effective search space used:    74214
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 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