GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Shewanella sp. ANA-3

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 7026102 Shewana3_3244 FAD dependent oxidoreductase (RefSeq)

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



>FitnessBrowser__ANA3:7026102
          Length = 491

 Score =  142 bits (359), Expect = 2e-38
 Identities = 120/409 (29%), Positives = 182/409 (44%), Gaps = 53/409 (12%)

Query: 22  PALQDDVETDVCVIGAGYTGLSSALFL--LENGFKVTVLEAAKVGFGASGRNGGQIVNSY 79
           P L+ D+  DV +IGAGY+GL +A +L   +    V +LEA  +G GASGRNGG ++ S+
Sbjct: 21  PPLEQDITADVAIIGAGYSGLWTAYYLKQYQPNLSVVILEAEYIGQGASGRNGGWLMGSF 80

Query: 80  SRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGVF--AALTAKQMG 137
           S D+  + R  G +Q  +   +  E    +    AK+ I CDL  GG    AA   +Q+ 
Sbjct: 81  SGDVAYLNRLEG-EQRLIAKAIIQETISEVATVCAKHHIDCDLHHGGNLRVAARYPEQLA 139

Query: 138 HLESQKRLW--ERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHPLNLALGEAAA 195
           +++++   W  + FG   +  LD+  + + V+  E    +       IHP  L  G A  
Sbjct: 140 NIKAELAQWRADGFGEEDIRWLDKTELDKQVSMAEGQAALFTPHCARIHPAKLVCGLADL 199

Query: 196 VESLGGVIYEQSPAVRIER--GASPVVHTPQGKVRAKFIIVAGNAYLGNLVPELAAKSMP 253
           V+SLG  IYE++    +     A   + TPQG VRA  ++ A   YL  L   L   ++P
Sbjct: 200 VQSLGVKIYERTSVNHMAHLGDALTQLQTPQGNVRAAIVVPAVEGYLRQL-SGLGRFTLP 258

Query: 254 CGTQVIATEPLGDELAHSL-LPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVYGARDPAN 312
             + +IATEPL +    ++ L       D + ++ Y + + D RLIFG    YG      
Sbjct: 259 VQSLLIATEPLTNVTWDAIGLANRATFSDASRIVTYGQRSPDNRLIFGARGGYGFGAKIR 318

Query: 313 IEAIIRPK---------------------------MLKAFPQLKDVKIDYAWTGNFLLTL 345
            E    PK                           +L  FPQLK V+I + W G   L  
Sbjct: 319 TEFGFDPKLFNGKFPVNQSPPQCAFEGEFGFRYQLLLALFPQLKGVQITHGWGGTLALAR 378

Query: 346 SRLPQ--------VGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQ 386
              P         +G +G       G  G GV   +L  + L + + G+
Sbjct: 379 RFAPHAIFDQSLGLGLIG-------GYGGEGVGAANLFARTLVDLILGR 420


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: 542
Number of extensions: 34
Number of successful extensions: 7
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: 491
Length adjustment: 33
Effective length of query: 394
Effective length of database: 458
Effective search space:   180452
Effective search space used:   180452
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