GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Burkholderia phytofirmans PsJN

Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate BPHYT_RS16285 BPHYT_RS16285 branched-chain amino acid aminotransferase

Query= BRENDA::P54691
         (305 letters)



>FitnessBrowser__BFirm:BPHYT_RS16285
          Length = 307

 Score =  182 bits (461), Expect = 1e-50
 Identities = 105/301 (34%), Positives = 168/301 (55%), Gaps = 12/301 (3%)

Query: 9   YFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAK 68
           + + K + + DAKI V TH LHYG   F G+R     +  G   +FRL  H  RL  SAK
Sbjct: 11  WMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTAD--GGTAIFRLQEHTKRLLNSAK 68

Query: 69  FLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFLVY- 123
               D+    E +     + V++N+ + S Y+RP+++  S  LG++ + + +      + 
Sbjct: 69  IFQMDVPFDHETLAAAQCEVVRENKLE-SCYLRPIIWVGSEKLGVSAKGNTIHVAIAAWP 127

Query: 124 -GLEMGDYLAADGVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAILM 182
            G  +G+   A G+  + SS+ R       +R K S  Y+ S LA  EA+  G+DEA+L+
Sbjct: 128 WGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALLL 187

Query: 183 NSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDKSE 242
           +  G V E +G N F+V NG++ TP +    L+GITRD+++T+A D GI   ++ I + E
Sbjct: 188 DVDGYVSEGSGENFFLVNNGKLYTP-DLSSCLDGITRDTVITLARDAGIQVIEKRITRDE 246

Query: 243 LMIADEVFLSGTAAKITPVKRIENFTLGGDR--PITEKLRSVLTAVTENREPKYQDWVFK 300
           +   DE F +GTAA++TP++ ++N T+G     PITEKL+S    +   +  KY +W+ K
Sbjct: 247 VYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKYANWLTK 306

Query: 301 I 301
           I
Sbjct: 307 I 307


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: 244
Number of extensions: 13
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: 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