GapMind for Amino acid biosynthesis

 

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

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

Query= BRENDA::P0AB80
         (309 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3369
          Length = 305

 Score =  291 bits (744), Expect = 2e-83
 Identities = 136/299 (45%), Positives = 203/299 (67%), Gaps = 1/299 (0%)

Query: 9   IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68
           IW +G+MV W DAK+HV++H LHYG   FEG+R Y++  G  +FR  EH  RL +SAKI 
Sbjct: 8   IWMDGQMVDWRDAKIHVLTHTLHYGCGAFEGVRAYNTANGTAIFRLEEHTDRLFNSAKIL 67

Query: 69  RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128
           R  +  + +E+ EA + V+R+N L S Y+RPL ++G   +GV+P  G    +++AA+ WG
Sbjct: 68  RMKIPFTKEEVNEAQKAVVRENKLESCYLRPLTWIGSQKLGVSPK-GNQIHLMVAAWAWG 126

Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188
           AYLG E L++GI    SS+ R   N   T AKA  NY +S+L   EA   GY E + LD 
Sbjct: 127 AYLGEEGLKRGIRVKTSSYTRHHVNITMTQAKAVSNYTNSILANMEALDDGYDEALLLDS 186

Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248
           +G++SEGAGEN+F +K+GV++TP  ++ AL GITR+ +  +AK+LG+E+ ++ ++R+ +Y
Sbjct: 187 SGFVSEGAGENIFVIKNGVIYTPDLSAGALNGITRNTVFHIAKDLGLEIVQKRITRDEVY 246

Query: 249 LADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLDQV 307
           +ADE F +GTAAE+TP+R +D I++G G  GP+T++IQ AFF +  G   +   WL +V
Sbjct: 247 IADEAFFTGTAAEVTPIRELDRIELGSGSRGPITEKIQSAFFDIVNGRNSNYAHWLTKV 305


Lambda     K      H
   0.319    0.136    0.413 

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: 300
Number of extensions: 11
Number of successful extensions: 2
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: 309
Length of database: 305
Length adjustment: 27
Effective length of query: 282
Effective length of database: 278
Effective search space:    78396
Effective search space used:    78396
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