GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Chromobacterium vaccinii MWU205

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_046157099.1 VL52_RS11115 FAD-binding oxidoreductase

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



>NCBI__GCF_000971335.1:WP_046157099.1
          Length = 429

 Score =  401 bits (1030), Expect = e-116
 Identities = 207/425 (48%), Positives = 278/425 (65%), Gaps = 1/425 (0%)

Query: 2   ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61
           A+ P+P SYYAA+A+   P+P L+ +   DVCV+G G  GLS+AL L E GF V +LE +
Sbjct: 5   AHQPHPPSYYAATAHAWDPQPPLRGEASCDVCVVGGGLAGLSAALNLREKGFSVILLEGS 64

Query: 62  KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121
            VGFGASGRNGGQ++  Y+ D+D I   VG + A+ L +M+ E   II ERV ++ IQCD
Sbjct: 65  HVGFGASGRNGGQVIAGYAGDMDGIRAQVGEEAAKALWDMSVEAVEIIDERVRRHGIQCD 124

Query: 122 LKDGGVFAALTAKQMGHLES-QKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180
            + G V AA+  + M  LE  Q+   ER+ +  ++L D+  +R  +A E Y GG+ D   
Sbjct: 125 WQRGYVSAAVKPRHMRELEDWQREAEERYDYGGMQLWDRAALRGKLASERYQGGLFDPRS 184

Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240
           GH+HPLN  LG A A  + G  I+EQ+PA+RIE+G +P V T  G VR + +++A N+Y+
Sbjct: 185 GHLHPLNYTLGLARAALAAGVDIHEQTPALRIEQGDAPKVFTEHGVVRCRHLVLACNSYI 244

Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300
           G L P L  + MP GT VIATEPLG+E A +L+  +  V D N++LDYYRL+ D RL+FG
Sbjct: 245 GALAPRLERRIMPAGTYVIATEPLGEERARALIADNMAVCDTNFVLDYYRLSADHRLLFG 304

Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360
           G V Y   +P ++   +R  ML+ FPQL DV IDYAW G   +T++R P  GRL  N+YY
Sbjct: 305 GKVSYSGHEPRDLAGSMRADMLRVFPQLADVGIDYAWGGFCDITVNRAPDFGRLSGNVYY 364

Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYG 420
            QG SGHGV  T LAGKV+AEA+ G + R D FA + H  FPGG+LLRTP   +G  YY 
Sbjct: 365 LQGFSGHGVNITGLAGKVVAEAIAGTSSRLDLFAKIRHRDFPGGKLLRTPALVLGMAYYR 424

Query: 421 LRDKL 425
           +RD L
Sbjct: 425 MRDYL 429


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: 627
Number of extensions: 29
Number of successful extensions: 2
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: 429
Length adjustment: 32
Effective length of query: 395
Effective length of database: 397
Effective search space:   156815
Effective search space used:   156815
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