GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Sinorhizobium meliloti 1021

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate SMc01578 SMc01578 aspartate aminotransferase

Query= curated2:B1I544
         (392 letters)



>FitnessBrowser__Smeli:SMc01578
          Length = 400

 Score =  164 bits (415), Expect = 4e-45
 Identities = 121/398 (30%), Positives = 186/398 (46%), Gaps = 19/398 (4%)

Query: 1   MSFVEAKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKI 60
           M+F+ A  +  + P     + Q   + KA+G DVI LG G+PD  TPD+I +AA   +  
Sbjct: 1   MAFL-ADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAID- 58

Query: 61  PANHQYPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDV 120
               +Y   +G+P  R A+A  + R   ++    + +V   G K+ + +     ++PGD 
Sbjct: 59  RGETKYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGT-GGKQILFNAFMATLNPGDE 117

Query: 121 VLVPDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPT 180
           V++P P +  Y     L GG P  VP    N F      +      + K    N P+NP+
Sbjct: 118 VVIPAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPS 177

Query: 181 GAVASKEFFARVVDFAREYG-ILVCHDAAYSEIAFDGYRPPSFLEVA-GAREVGIEFHSV 238
           GA  S E    + D   ++  + V  D  Y  + +  +R  + +EV  G  E  +  + V
Sbjct: 178 GAAYSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGV 237

Query: 239 SKTYNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEM 298
           SK Y MTGWR G+AAG    ++A+  ++    SG   + Q+AA+ ALNGPQD +    E+
Sbjct: 238 SKAYAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEI 297

Query: 299 YRERRDLVVDTLNDL-GWRLTRPRATFYIW--------APVPAG---HDASSFAEMVLEK 346
           ++ RRDLVV  LN   G     P   FY++           P+G        F   +LE 
Sbjct: 298 FQGRRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLET 357

Query: 347 AGVVITPGTGYGTYGEGYFRISLTLPTPRLVEAMERLR 384
            GV +  G+ +G      FRIS       L EA  R++
Sbjct: 358 EGVAVVHGSAFGLGPN--FRISYATSEALLEEACRRIQ 393


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: 312
Number of extensions: 21
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: 400
Length adjustment: 31
Effective length of query: 361
Effective length of database: 369
Effective search space:   133209
Effective search space used:   133209
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