GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Acidovorax sp. GW101-3H11

Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Ac3H11_3369 Branched-chain amino acid aminotransferase (EC 2.6.1.42)

Query= BRENDA::P54691
         (305 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3369
          Length = 305

 Score =  184 bits (466), Expect = 3e-51
 Identities = 113/303 (37%), Positives = 170/303 (56%), Gaps = 16/303 (5%)

Query: 9   YFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAK 68
           + + + V + DAKI V TH LHYG  AF G+R        GT + FRL+ H DRL  SAK
Sbjct: 9   WMDGQMVDWRDAKIHVLTHTLHYGCGAFEGVRAYNTAN--GTAI-FRLEEHTDRLFNSAK 65

Query: 69  FLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVY--SSGLGIAPRLHNLEKDFLVYG 124
            L   I  + E++ E     V++N+ + S Y+RPL +  S  LG++P+ + +    +V  
Sbjct: 66  ILRMKIPFTKEEVNEAQKAVVRENKLE-SCYLRPLTWIGSQKLGVSPKGNQIH--LMVAA 122

Query: 125 LEMGDYLAADG----VSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFDEAI 180
              G YL  +G    +  + SS+ R        + K  + Y  S LA  EA++ G+DEA+
Sbjct: 123 WAWGAYLGEEGLKRGIRVKTSSYTRHHVNITMTQAKAVSNYTNSILANMEALDDGYDEAL 182

Query: 181 LMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRPIDK 240
           L++S G V E  G N+F+++NG I TP      L GITR+++  IA DLG+   Q+ I +
Sbjct: 183 LLDSSGFVSEGAGENIFVIKNGVIYTPDLSAGALNGITRNTVFHIAKDLGLEIVQKRITR 242

Query: 241 SELMIADEVFLSGTAAKITPVKRIENFTLG-GDR-PITEKLRSVLTAVTENREPKYQDWV 298
            E+ IADE F +GTAA++TP++ ++   LG G R PITEK++S    +   R   Y  W+
Sbjct: 243 DEVYIADEAFFTGTAAEVTPIRELDRIELGSGSRGPITEKIQSAFFDIVNGRNSNYAHWL 302

Query: 299 FKI 301
            K+
Sbjct: 303 TKV 305


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: 229
Number of extensions: 12
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: 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