GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Shewanella amazonensis SB2B

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 6938339 Sama_2458 FAD dependent oxidoreductase (RefSeq)

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



>FitnessBrowser__SB2B:6938339
          Length = 442

 Score =  155 bits (392), Expect = 2e-42
 Identities = 136/430 (31%), Positives = 202/430 (46%), Gaps = 21/430 (4%)

Query: 2   ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFL-LENGFKVTVLEA 60
           A    P ++++ +  P+P  P LQ  ++TDV VIG G+TGL +A +L  E G +VT+LEA
Sbjct: 11  AQQALPSTFWSGTTEPLPESPRLQGHLQTDVIVIGGGFTGLLTAYYLATEYGRQVTLLEA 70

Query: 61  AKVGFGASGRNGGQIVNSYSR-DIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQ 119
            ++GFGAS RNGG ++    R     + +      A+ +     E    +   +   +I 
Sbjct: 71  NRIGFGASARNGGFVLKGSGRLGYGQMAKRWDLDTAKGIYQEFSEAVARVEGLIQDGKID 130

Query: 120 CDLKDGGVF-AALTAKQMGHLESQKRLWERFGHTQLELLDQRRIR-EVVACEEYVGGMLD 177
           C+ ++ G    A + K M  L++      R      E +   R+R + +   +  G +  
Sbjct: 131 CNPQEKGYLKIAHSPKAMKTLQAGADFIARHMGQGAEFICPARLRIDYLNHHQSYGALRL 190

Query: 178 MSGGHIHPLNLALGEAAAVESLGGVIYEQS---PAVRIERGASPVVHTPQGKVRAKFIIV 234
             G  ++PL L  G A      G  I+EQS    +VR  +G S  + T  G++ A  ++ 
Sbjct: 191 ADGFGLNPLKLLQGYARLAREAGVQIFEQSTVLASVRTAKGFS--LETEAGRIDANAMVF 248

Query: 235 AGNAYL-GNLVPELAAKSMPCGTQVIATEPLGDE-LAHSLLPQDYCVEDCNYLLDYYRLT 292
           AGNAY    L   L  + +P  + VI TEPL +  LA + L       D   L  YYRL 
Sbjct: 249 AGNAYTQPGLTETLTGRFLPILSNVIVTEPLSEAVLAEAGLYSRQVAMDTRILKYYYRLL 308

Query: 293 GDKRLIFGG-GVVYGARDPAN--IEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLP 349
            + RL+FGG G V+G RD  N    A ++  M KAFP L DV + + W G    +L  +P
Sbjct: 309 PENRLLFGGRGAVWG-RDADNSVYPARLKEAMNKAFPALTDVGLSHTWHGWLAASLDDMP 367

Query: 350 QVGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRT 409
            V   G    YS G  G GV+++  A   LA  L G+A        LP Y  P       
Sbjct: 368 HVYTRGGE-GYSLGYCGAGVSFSSQAAWRLAGMLSGKAA-----PSLPLYGTPLPAFPLA 421

Query: 410 PFAAMGAWYY 419
           P   +G W +
Sbjct: 422 PLRRVGQWAF 431


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: 549
Number of extensions: 31
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: 442
Length adjustment: 32
Effective length of query: 395
Effective length of database: 410
Effective search space:   161950
Effective search space used:   161950
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