GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Alicycliphilus denitrificans K601

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_013518247.1 ALIDE2_RS17665 FAD-binding oxidoreductase

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



>NCBI__GCF_000204645.1:WP_013518247.1
          Length = 432

 Score =  201 bits (511), Expect = 4e-56
 Identities = 142/430 (33%), Positives = 213/430 (49%), Gaps = 8/430 (1%)

Query: 1   MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEA 60
           +A+ P   S +AA+A   P  PAL   V TDV V+GAGYTGLS+AL L E+G +V VL+A
Sbjct: 6   IASHPAAPSLWAATAPAAPDTPALGASVSTDVLVVGAGYTGLSTALHLAESGARVCVLDA 65

Query: 61  AKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQC 120
              G+GASGRNGGQ+  +   D D + R  G ++A+ L +       ++   +A++ I C
Sbjct: 66  HAPGWGASGRNGGQVNPTLKYDPDDLVRIYGAERAEPLIDTVSRSADLVYGLIARHAIDC 125

Query: 121 -DLKDGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMS 179
             ++ G +    T   +  + ++ R WER G  ++E+LD+  +   +    + GG LD  
Sbjct: 126 APVRAGWLQVGYTQHAVDGMHARARQWERRG-VRVEMLDRAAVAARIGTPAFAGGWLDGR 184

Query: 180 GGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIER-GASPVVHTPQG-KVRAKFIIVAGN 237
            G + PL  A G A A + LG  ++  SP V +ER G   +  T QG +V+A+ +++  N
Sbjct: 185 AGGVQPLAYARGLARAAQGLGVQVHGGSPVVALERQGMHWIATTAQGHRVQAQQVVLGTN 244

Query: 238 AYLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRL 297
            Y   L P LA   +   + ++AT PLG      +LP          LL Y+R     RL
Sbjct: 245 GYTDGLWPGLARTVLAANSFIVATRPLG-PAGDGILPGGETGSTSQRLLLYFRKDAQGRL 303

Query: 298 IFGG-GVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD 356
           + GG G     + P +   + R   L  FPQL  ++ +Y W G   +T   +P + R   
Sbjct: 304 LMGGRGHFADPQGPQDFSHLERAVAL-MFPQLGPLQYEYRWAGRIAVTRDFMPHLHRPAP 362

Query: 357 NIYYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGA 416
            I  + G +G G+      G+  A  + G +     F   P  P P   L R   AA  A
Sbjct: 363 GITMALGYNGRGIAMATSLGRHAAALVAGSSAAACPFPVTPVQPIPLHGLQRFYIAAGVA 422

Query: 417 WYYGLRDKLG 426
           W Y L D+LG
Sbjct: 423 W-YSLLDRLG 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: 538
Number of extensions: 30
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: 427
Length of database: 432
Length adjustment: 32
Effective length of query: 395
Effective length of database: 400
Effective search space:   158000
Effective search space used:   158000
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 Apr 09 2024. 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