GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Acidovorax sp. GW101-3H11

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate Ac3H11_1602 Aspartate aminotransferase (EC 2.6.1.1)

Query= curated2:B1I544
         (392 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1602
          Length = 408

 Score =  178 bits (451), Expect = 3e-49
 Identities = 130/401 (32%), Positives = 194/401 (48%), Gaps = 21/401 (5%)

Query: 2   SFVEAKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIP 61
           +F  A R+  +      R+ Q     K QG  VI LG+G+PD  TP HI+EAA++ +   
Sbjct: 9   AFRAADRLGAIGVSEIVRLTQEANQLKRQGQPVIVLGLGEPDFDTPAHILEAAQQAMARG 68

Query: 62  ANHQYPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVV 121
             H Y    G    + A+   +    G++     E+ +  G+K+ + +     V+PGD V
Sbjct: 69  ETH-YTVLDGTAELKAAIQHKFKHYNGLDFQ-LNEITAGAGAKQILYNALMASVNPGDEV 126

Query: 122 LVPDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTG 181
           ++P P +  YA   ++AGG+P  VP T  NGF      + A    R + +FIN P+NP+G
Sbjct: 127 ILPAPYWTSYADMVLIAGGVPVVVPCTEANGFRITPEQLEAAITPRTRWVFINSPSNPSG 186

Query: 182 AVASKEFFARVVDFAREYG-ILVCHDAAYSEIAFDG--YRPPSFLEVAGAREVGIEFHSV 238
           A  S E    V++    +  + +  D  Y  I +DG  +  P+ + +   R+  +  + V
Sbjct: 187 AAYSAEQLRPVLEVVERHPQVWLLADDIYEHILYDGRAFATPAAV-LPSLRDRTLTVNGV 245

Query: 239 SKTYNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEM 298
           SK Y MTGWR G+ AG    + A+  ++S   S    + Q AA+AAL GPQD V+  C+ 
Sbjct: 246 SKAYAMTGWRLGYGAGPKALIAAMAVVQSQATSCPSSISQAAAVAALTGPQDVVRERCQA 305

Query: 299 YRERRDLVVDTLN-DLGWRLTRPRATFYIWA--------PVPAG---HDASSFAEMVLEK 346
           +++RRDLVV  LN   G R   P   FY +A          P G      + F   +L +
Sbjct: 306 FQDRRDLVVAALNVSPGLRCRVPEGAFYTFASCEGALGRTTPGGLLLRTDADFCAYLLRE 365

Query: 347 AGVVITPGTGYGTYGEGYFRISLTLPTPRLVEAMERL-RGC 386
             V + PG   G     YFRIS    T  L EA  R+ R C
Sbjct: 366 HHVAVVPGGVLGL--APYFRISYAASTADLQEACARIQRAC 404


Lambda     K      H
   0.321    0.139    0.430 

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: 318
Number of extensions: 13
Number of successful extensions: 3
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: 392
Length of database: 408
Length adjustment: 31
Effective length of query: 361
Effective length of database: 377
Effective search space:   136097
Effective search space used:   136097
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: 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 (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