GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Desulfovibrio vulgaris Miyazaki F

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)

Query= curated2:B1I544
         (392 letters)



>FitnessBrowser__Miya:8501474
          Length = 390

 Score =  185 bits (470), Expect = 2e-51
 Identities = 118/386 (30%), Positives = 195/386 (50%), Gaps = 17/386 (4%)

Query: 8   RIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYP 67
           R+  + P     +     + KA+GV V+SL +G+PD PTP+H+ EAA+  +      +Y 
Sbjct: 6   RLTRIKPSATLAVNAKALELKAKGVQVVSLAVGEPDFPTPEHVREAAKTAID-QGFTRYT 64

Query: 68  SSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPG 127
              G+P  R+AV  ++AR +GVE  P    V   G K+ + +L  C ++PGD VLVP P 
Sbjct: 65  QVPGIPELRQAVCGYFARFYGVEA-PMEATVVTNGGKQALYNLFQCLLNPGDEVLVPAPY 123

Query: 128 YPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKE 187
           +  Y     LAGG+P  V   A  GF      +      + +V+ +N P+NPTGA  S+ 
Sbjct: 124 WVSYPALVELAGGVPVFVASPAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGACYSRA 183

Query: 188 FFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIE----FHSVSKTYN 243
               ++++A    + V  D  Y  +    Y P   + V    E   E     + ++KT+ 
Sbjct: 184 ETDAIMEWAIARDLFVVSDEIYDRLV---YEPAEAVSVCDWWERHPENVAVVNGLAKTFA 240

Query: 244 MTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERR 303
           MTGWR G+A  +   ++A+ +++    S +  V Q AA+AAL GP D V+ + + +R RR
Sbjct: 241 MTGWRVGYALAHPDLIKAMTKIQGQSTSNICSVAQKAALAALTGPYDAVEEMKKSFRRRR 300

Query: 304 DLVVDTLNDL-GWRLTRPRATFYIWAPV-----PAGHDASSFAEMVLEKAGVVITPGTGY 357
           DL    ++   G    +P   FY++A +     PA  D++S    ++E+A V + PG  +
Sbjct: 301 DLAHGIVSSWPGVICPKPDGAFYLFADMRALFTPALPDSASLCTYIMEQANVALVPGAAF 360

Query: 358 GTYGEGYFRISLTLPTPRLVEAMERL 383
           G   +   R S  +    L+ A++++
Sbjct: 361 G--DDACLRFSYAVSDDTLMIALDKV 384


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: 316
Number of extensions: 14
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: 390
Length adjustment: 31
Effective length of query: 361
Effective length of database: 359
Effective search space:   129599
Effective search space used:   129599
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