GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Pedobacter sp. GW460-11-11-14-LB5

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate CA265_RS15785 CA265_RS15785 branched-chain-amino-acid transaminase

Query= BRENDA::P0AB80
         (309 letters)



>FitnessBrowser__Pedo557:CA265_RS15785
          Length = 296

 Score =  176 bits (446), Expect = 6e-49
 Identities = 100/263 (38%), Positives = 148/263 (56%), Gaps = 8/263 (3%)

Query: 9   IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68
           I+ +G+  +  ++   +   +LHYG + FEGIR Y +H G  +F+   H  RL  S ++ 
Sbjct: 10  IYLDGQFEKAVNSSTDLYGQSLHYGYAAFEGIRAYKTHNGNRIFKAAAHFDRLERSCQLA 69

Query: 69  RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128
             P      EL+ A   +++ N L  AYIRPL+F     M +N P+G S  ++I A+ W 
Sbjct: 70  NIPFPWDKQELIAATYKLLQLNKLKDAYIRPLVFCHP-NMKLNEPSGVS--ILICAWEWD 126

Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188
           AY G + L+      VS + R  P +IP  AK  GNY++S+L  + A   GY E + LD+
Sbjct: 127 AYSGNKLLK----LTVSDYERPNPKSIPMEAKLSGNYVNSILATTAANIKGYDEALLLDM 182

Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248
           +G+++E +G N+F  KDG LFTP    + LPGITR  + +L   L IE  E+ L+ E L 
Sbjct: 183 HGFVAEASGANIFLEKDGKLFTPSL-GNILPGITRATVKELCTVLDIECIEKKLTIEDLK 241

Query: 249 LADEVFMSGTAAEITPVRSVDGI 271
            AD  F+ GTA EI  + S+D I
Sbjct: 242 NADSAFLCGTATEIAGIASIDDI 264


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: 197
Number of extensions: 13
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: 309
Length of database: 296
Length adjustment: 27
Effective length of query: 282
Effective length of database: 269
Effective search space:    75858
Effective search space used:    75858
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