GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Cupriavidus basilensis 4G11

Align Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase; PhPPA-AT; EC 2.6.1.1; EC 2.6.1.78; EC 2.6.1.79 (characterized)
to candidate RR42_RS02275 RR42_RS02275 aspartate aminotransferase

Query= SwissProt::E9L7A5
         (479 letters)



>FitnessBrowser__Cup4G11:RR42_RS02275
          Length = 397

 Score =  163 bits (412), Expect = 1e-44
 Identities = 118/373 (31%), Positives = 184/373 (49%), Gaps = 23/373 (6%)

Query: 102 GVP-VIRLAAGEPDFDTPAPIVEAGINAIREGHTRYTPNAGTMELRSAISHKLKEENGLS 160
           G+P V+    GE D  TPA I +A   A+  G T YT N G   LRSA++  +   +G +
Sbjct: 36  GLPDVLPFWFGESDQVTPAFIRDAASRALAGGATFYTHNLGIAPLRSALADYVSALHGAT 95

Query: 161 YTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPAPYWVSYPEMARLADATPVILPTSI-S 219
              D ++V++    +++ A   V  PGD  +   P W +  E+ ++  A    +     +
Sbjct: 96  AL-DNVVVTSAGVNALMLAAQLVAGPGDRAVAVTPLWPNLVEIPKILGAEVETVSLDYGA 154

Query: 220 EDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPRKLLEQIAEIVARHPRLLVISDEIY 279
             + LD   L + LT  +RLL++ SP+NPTG V  R   + +     RH  + +I+DE+Y
Sbjct: 155 HGWTLDLDKLLAALTPDTRLLMINSPNNPTGWVMSRADQQAVLAHCRRHG-IWIIADEVY 213

Query: 280 EHIIYAP---ATHTSFASLPGMWDRTLTVNGFSKAFAMTGWRLGYIAGPKHFIAACNKIQ 336
           E + Y     A   SF  +    +R + VN FSKA+ MTGWRLG++  P        K+ 
Sbjct: 214 ERLYYGKGDGAIAPSFLDIASRDERVICVNSFSKAWLMTGWRLGWMVLPAALTDDLGKLV 273

Query: 337 SQFTSGASSISQKAAVAALGLGYAGGELVATMVKSFRERRDYLVKSFGEIEGVKISEPRG 396
              TS A S  Q+A + A+  G A       +V   R  RD+LV +   + GV +  P G
Sbjct: 274 EYNTSCAPSFVQEAGIVAVREGEA---FTRELVGRLRAARDHLVSALAVVPGVDVHAPEG 330

Query: 397 AFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQVALVPGDAFGD--DTCIRISYAA 454
           A Y+F  L+             ++S +LC+ L+ +A++ L PG AFGD  +  +R  YA 
Sbjct: 331 AMYVFFRLA-----------GASDSLALCKQLVREARLGLAPGSAFGDEGEGFVRWCYAC 379

Query: 455 SLSTLQAAVERIK 467
             + L   V R++
Sbjct: 380 DPARLDEGVRRLR 392


Lambda     K      H
   0.317    0.132    0.375 

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: 388
Number of extensions: 22
Number of successful extensions: 8
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: 479
Length of database: 397
Length adjustment: 32
Effective length of query: 447
Effective length of database: 365
Effective search space:   163155
Effective search space used:   163155
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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