GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Dechlorosoma suillum PS

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate Dsui_0132 Dsui_0132 aspartate/tyrosine/aromatic aminotransferase

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__PS:Dsui_0132
          Length = 385

 Score =  176 bits (447), Expect = 8e-49
 Identities = 119/359 (33%), Positives = 180/359 (50%), Gaps = 10/359 (2%)

Query: 23  LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82
           L AQ  D+I + +G+PDF TP  + AAA++ + +    YTP  G  ELR+A+  + +++ 
Sbjct: 26  LEAQGRDIIHMEVGEPDFPTPEPILAAAREFLQDGRVFYTPALGLPELREAISGFYRQRY 85

Query: 83  DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142
                A S I IT GAS A+  A   + +PG E ++  P YP     +      PV +  
Sbjct: 86  GIAVPA-SRIAITAGASGALTLALACLAAPGSEWLLTDPGYPCNRHFVRAFEGVPVSIPV 144

Query: 143 -TSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDE 201
             +  F+ T   +E      T   +   P+NPTG  L   EL  IA  ++ R   ++ DE
Sbjct: 145 GAASNFQPTRLDLEQHWNERTAGALFASPANPTGTMLDAAELADIADFVRQRQGQLIIDE 204

Query: 202 IYSELTY--DRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQY 259
           IY  LTY  D P    A    D   V+   SK   MTGWR+G+L  P+   + + K+ Q 
Sbjct: 205 IYHGLTYNGDAP---TALAAGDNIFVVQSFSKYFQMTGWRLGWLVIPEPFVRDVEKLAQN 261

Query: 260 NVSCASSISQKAALEAVTNGFDDALIMRE-QYKKRLDYVYDRLVSMGLDV-VKPSGAFYI 317
               AS+ +Q AAL A        L  R  ++K R DY+   L ++G  +  +P GAFY+
Sbjct: 262 LFISASTPAQHAALAAFQPETIALLEQRRAEFKARRDYLAPALEAIGFRITAQPEGAFYL 321

Query: 318 FPSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYG-EGYVRLSFACSMDTLREGLDRL 375
           +    +    SF F+  LLE+AGVA+ PG  F  +G   +VR ++  +   L EG++R+
Sbjct: 322 YADCSTLTDDSFGFARRLLEEAGVAITPGIDFGNHGASSHVRFAYTNAQARLAEGVERI 380


Lambda     K      H
   0.319    0.135    0.388 

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: 5
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: 393
Length of database: 385
Length adjustment: 30
Effective length of query: 363
Effective length of database: 355
Effective search space:   128865
Effective search space used:   128865
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