GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Azospirillum brasilense Sp245

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate AZOBR_RS25655 AZOBR_RS25655 oxidoreductase

Query= reanno::pseudo5_N2C3_1:AO356_21495
         (427 letters)



>FitnessBrowser__azobra:AZOBR_RS25655
          Length = 426

 Score =  208 bits (529), Expect = 3e-58
 Identities = 127/405 (31%), Positives = 205/405 (50%), Gaps = 4/405 (0%)

Query: 7   PESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFG 66
           P+S + A+A P P  P L+D VE D+ VIG G+TGLS+AL   E+G +  VLEA+++G G
Sbjct: 5   PDSLWEATAPPPPALPVLKDSVEADLLVIGGGFTGLSAALHAAESGKRAVVLEASEIGRG 64

Query: 67  ASGRNGGQIVNSYSR-DIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125
           ASGRN GQ++ + +R D + +    G ++ +    +  +    +   + +  I C  +  
Sbjct: 65  ASGRNNGQVIPTLTRPDPEDLIAKFGQERGERFVALIRDSAETLFALIRRLNIDCAAEQT 124

Query: 126 G-VFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIH 184
           G V    +  ++   E + + W   G   +ELLD+  I  ++  + Y GG ++ SGGHI+
Sbjct: 125 GWVQPVHSPGRIAIAERRAKQWGSRG-APVELLDRAGISALLGTDAYYGGWMNRSGGHIN 183

Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIER-GASPVVHTPQGKVRAKFIIVAGNAYLGNL 243
           PL LA G A      G  ++  SP + +ER G   V  TP G V    +++  N Y   +
Sbjct: 184 PLALARGLAGKAVEAGASVFINSPVLSVERRGDRWVARTPDGTVTTHALVLGTNGYAAAV 243

Query: 244 VPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGV 303
            PE+  + +P  +  +AT+PL +    S+LP    + D +  L + R T D RL+ GG +
Sbjct: 244 FPEIRTEVVPVLSWQMATQPLDEAQRRSILPGRQAMSDTHGDLRFMRYTADHRLVSGGAL 303

Query: 304 VYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQG 363
           +        +  I+  ++   FP L+ ++ DY W G   +T    P+V +LG N +   G
Sbjct: 304 LVPVDGADRLRRIVGLRLASMFPTLRGLRFDYVWNGRIAMTTDYTPRVHQLGPNAFTWAG 363

Query: 364 CSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLR 408
           C+G GV  +   G+ LA A  G+     A       P P   LL+
Sbjct: 364 CNGRGVALSVSLGRELAYAALGRDPAELALPLTEPRPLPFNDLLQ 408


Lambda     K      H
   0.320    0.139    0.421 

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: 516
Number of extensions: 23
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: 427
Length of database: 426
Length adjustment: 32
Effective length of query: 395
Effective length of database: 394
Effective search space:   155630
Effective search space used:   155630
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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