GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Pseudomonas fluorescens GW456-L13

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate PfGW456L13_2943 Aspartate aminotransferase (EC 2.6.1.1)

Query= curated2:B1I544
         (392 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2943
          Length = 395

 Score =  181 bits (460), Expect = 2e-50
 Identities = 122/362 (33%), Positives = 177/362 (48%), Gaps = 5/362 (1%)

Query: 28  KAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYPSSAGMPAYRRAVADWYARRF 87
           + QGVDV+ L IGDPD  TP  I++AA   L     H YP+  G    R ++A  + RR 
Sbjct: 28  REQGVDVLLLSIGDPDFDTPQPIVQAAIGSLLAGDTH-YPAVRGSQGLRDSIARHHRRRS 86

Query: 88  GVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGYPVYAGGTILAGGIPHPVPL 147
           G  +D Q  +V   G++  +  +  C +DPGD VLV +P Y  Y G     G    PVP+
Sbjct: 87  GQAVDAQHVIV-FPGAQCAVYSVAQCLLDPGDEVLVAEPMYVTYEGVFGACGAKVVPVPV 145

Query: 148 TAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKEFFARVVDFAREYGILVCHDA 207
            + NGF  D A + A      + M +N PNNP+GA      +  +      + + +  D 
Sbjct: 146 RSQNGFRVDPADVAALITPNTRAMLLNSPNNPSGASLPLTAWKALAALCIRHDLWLISDE 205

Query: 208 AYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTGWRAGWAAGNAGAVEALGRLKS 267
            YSE+ F+G    S   + G  E     +S+SK++ M+GWR GW  G     E L  L  
Sbjct: 206 VYSELLFEG-EHISPASLPGMAERTATINSLSKSHAMSGWRVGWVIGPQSLCEHLVNLSL 264

Query: 268 NLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVDTLNDL-GWRLTRPRATFYI 326
            +  G+   +Q AA  AL+     V  + E YR+RRDLV  +LN   G +  RP    ++
Sbjct: 265 CMLFGIPDFIQNAAQLALDENLPHVAQMREEYRQRRDLVCASLNLCPGIQAIRPDGGMFV 324

Query: 327 WAPV-PAGHDASSFAEMVLEKAGVVITPGTGYGTYGEGYFRISLTLPTPRLVEAMERLRG 385
              V   G  A  FAE +L+  GV +  G  +G    G+ RI L +  P+L +A  R+  
Sbjct: 325 MVDVRQTGLSAQHFAERLLDGYGVSVLAGEAFGPSAAGHIRIGLVVDRPKLADACRRIVM 384

Query: 386 CL 387
           C+
Sbjct: 385 CV 386


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: 310
Number of extensions: 16
Number of successful extensions: 4
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: 395
Length adjustment: 31
Effective length of query: 361
Effective length of database: 364
Effective search space:   131404
Effective search space used:   131404
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 Apr 09 2024. The underlying query database was built on Apr 09 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