GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Tatumella morbirosei LMG 23360

Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate WP_038021942.1 HA49_RS08155 FAD-binding oxidoreductase

Query= SwissProt::P37906
         (426 letters)



>NCBI__GCF_000757425.2:WP_038021942.1
          Length = 478

 Score =  173 bits (439), Expect = 9e-48
 Identities = 126/406 (31%), Positives = 199/406 (49%), Gaps = 6/406 (1%)

Query: 6   SSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIGFGA 65
           ++YY ++   +  F  +     C++ V+GGG  G S+ALHLAE+G D ++LE + IG GA
Sbjct: 48  ANYYESTLAPWMSFPAMETDKQCELVVIGGGLLGASTALHLAESGIDTILLEKNTIGSGA 107

Query: 66  SGRNGGQLVNSYSR-DIDVIEKSYGMDTARMLGSM-MFEGGEIIRERIKRYQIDCDYRPG 123
           SGRNGGQL    +R + + + ++   D AR L      E   +I E   RY +  D + G
Sbjct: 108 SGRNGGQLTPGLARWEAESMLENLSTDEARRLWRFTSAEAMGLIDEIAGRYDLQLDRQYG 167

Query: 124 GLFVAMNDKQLATLEEQKENWERYGNKQLELLDANAIRREVASDRYTGALLDHSGGHIHP 183
            L  A++   +  L +  +  +  G++Q+ +L    ++  + SD Y G +LD+ GG IH 
Sbjct: 168 HLTAAVHPGHMNALVQAADARKFLGDEQVTILGNYQLQDHINSDIYYGGVLDNCGGQIHS 227

Query: 184 LNLAIGEADAIRLNGGRVYELSAVTQIQHT-TPAVVRTAKGQVTAKYVIVAGNAYLGDKV 242
           L L  G      LNGG V+E S V +I+ + T   V TA G +TA   +V         +
Sbjct: 228 LALNRGLIYGFLLNGGCVHEHSEVIKIEESPTGTKVHTASGVITATRGVVIAVHDETHNL 287

Query: 243 EPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGGGV 302
             E +  ++P  T V  T  + E   +SL+P    V D    +DYYR   + RLL+GG  
Sbjct: 288 LNENSSTTLPFYTYVGVTSPV-EGGHQSLLPTGKPVYDTQLQIDYYRPVRNQRLLFGGQG 346

Query: 303 VYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTN--IYYM 360
                D       +  +L   F Q   +++D+ W+G   LTL+      +   +  IY +
Sbjct: 347 TGMRWDDTRTVDYLTSRLRTVFSQRDDIQLDFAWSGTTDLTLNGATDCRQNGAHGQIYSV 406

Query: 361 QGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTL 406
            G+SGHG+  T   G+ I + + G  + F    ++ H     GR L
Sbjct: 407 HGWSGHGIAQTVRIGKAITDDITGRNDDFKMLTSIKHTSLLLGRQL 452


Lambda     K      H
   0.320    0.138    0.411 

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: 544
Number of extensions: 32
Number of successful extensions: 5
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: 426
Length of database: 478
Length adjustment: 33
Effective length of query: 393
Effective length of database: 445
Effective search space:   174885
Effective search space used:   174885
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 24 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