GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Desulfovibrio vulgaris Miyazaki F

Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate 8501549 DvMF_2268 branched-chain amino acid aminotransferase (RefSeq)

Query= BRENDA::P54691
         (305 letters)



>FitnessBrowser__Miya:8501549
          Length = 307

 Score =  162 bits (410), Expect = 9e-45
 Identities = 97/302 (32%), Positives = 167/302 (55%), Gaps = 16/302 (5%)

Query: 9   YFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAK 68
           +F+ K VP+++A + V TH LHYG   F G+R     +  G   +FRL  H  RL  SAK
Sbjct: 9   WFDGKQVPWDEANVHVLTHTLHYGVGVFEGIRAYKCAD--GGSAVFRLREHMQRLLNSAK 66

Query: 69  FLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFLVYG 124
            L   I  + +++ + + + +K+N+  +  YIRPL +  +  +G+ P  + ++   ++  
Sbjct: 67  ILRMVIPYTVDQLVDAVEETLKRNKLAEG-YIRPLSFVGAGAMGVYPGDNPVQT--IIAT 123

Query: 125 LEMGDYLAAD----GVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAI 180
              G YL A+    G+  + SS+ R    +   + K    Y+ S LAK EA   G+DE +
Sbjct: 124 WPWGAYLGAEALEHGIRVKTSSFCRHHVNAMMTKAKACGNYVNSVLAKMEAKADGYDEGL 183

Query: 181 LMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDK 240
           ++++QG V EATG N+F+VR G+++       +L+GITR+S++T+A +LG    ++   +
Sbjct: 184 MLDTQGFVSEATGENIFIVR-GKLIKTTPLTSVLDGITRNSLITLARELGYEVVEQQFTR 242

Query: 241 SELMIADEVFLSGTAAKITPVKRIENFTLGGDR--PITEKLRSVLTAVTENREPKYQDWV 298
            EL IADE F  GTAA++TP++ ++   +G     P+T+ L+       +   P Y  W+
Sbjct: 243 DELYIADEAFFCGTAAELTPIREVDLRVIGQGTAGPVTKHLQGEYFKAVKGENPAYAHWL 302

Query: 299 FK 300
            +
Sbjct: 303 HR 304


Lambda     K      H
   0.320    0.138    0.406 

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: 192
Number of extensions: 9
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: 305
Length of database: 307
Length adjustment: 27
Effective length of query: 278
Effective length of database: 280
Effective search space:    77840
Effective search space used:    77840
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: 48 (23.1 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