GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Dyella japonica UNC79MFTsu3.2

Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate N515DRAFT_2015 N515DRAFT_2015 branched-chain amino acid aminotransferase

Query= BRENDA::P54691
         (305 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2015
          Length = 305

 Score =  135 bits (340), Expect = 1e-36
 Identities = 90/293 (30%), Positives = 145/293 (49%), Gaps = 17/293 (5%)

Query: 16  PFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAKFLHYDI- 74
           P+ +A   V +HALHYG++ F G+R    P+      +FRL  H  RL +SAK   YD+ 
Sbjct: 17  PWREATTHVMSHALHYGSSVFEGIRSYATPDGAA---IFRLTDHLKRLYQSAKI--YDMV 71

Query: 75  ---SAEKIKEVIVDFVKKNQPDKSFYIRPLVYSSGLGIAPRLHNLEKDFLVYGLEMGDYL 131
              S ++I     D +K+N    + Y+RP+ Y  GLG          D  V    MG YL
Sbjct: 72  LPYSQDQIAAACRDVIKQNGLGAA-YLRPVAYR-GLGGFGLSAETPIDVAVAAWPMGPYL 129

Query: 132 AAD----GVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAILMNSQGK 187
             +    G+   +SSW R    + P   K    Y++  L   EA   GF E I + + G 
Sbjct: 130 GPEALESGIDACVSSWQRFAPNTIPAGAKAGGNYLSGQLIAREARRLGFGEGIALANTGL 189

Query: 188 VCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDKSELMIAD 247
           + E  G N+F+V +G + T      IL GITR +++T+A + GI   +R I +  L + D
Sbjct: 190 LSEGAGENLFLVFDGVLHTTPASASILTGITRHTLITLAREDGIEVIERDIPREYLYLCD 249

Query: 248 EVFLSGTAAKITPVKRIENFTLGGDRP--ITEKLRSVLTAVTENREPKYQDWV 298
           E+ + GTAA+ITP++ ++   +G  +   +T +++ +   +   +      W+
Sbjct: 250 ELLMCGTAAEITPIRSVDGKKIGSGKAGRVTRRMQELFFGLFNGKTNDQWGWL 302


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: 224
Number of extensions: 9
Number of successful extensions: 3
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: 305
Length adjustment: 27
Effective length of query: 278
Effective length of database: 278
Effective search space:    77284
Effective search space used:    77284
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