GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Marivita geojedonensis DPG-138

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_085636469.1 MGEO_RS08635 FAD-binding oxidoreductase

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



>NCBI__GCF_002115805.1:WP_085636469.1
          Length = 434

 Score =  352 bits (904), Expect = e-101
 Identities = 180/426 (42%), Positives = 264/426 (61%), Gaps = 2/426 (0%)

Query: 2   ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61
           A   YP+S+YAA+A P+PP   LQ +   DVC+IGAGYTGLS+AL L E G  V +L+A 
Sbjct: 9   ARGSYPDSWYAATATPLPPFAPLQGETRADVCIIGAGYTGLSAALHLAEMGADVVLLDAH 68

Query: 62  KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121
           +VGFGASGRNGGQ+ +   +D   +E+ VG   A+ L ++  +   ++R+ VA++ + C 
Sbjct: 69  RVGFGASGRNGGQLGSGQRQDQITLEKLVGSDAARALWDLGEDSKTLVRDLVARHGLDCY 128

Query: 122 LKDGGVFAALTAKQMGHLESQ-KRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180
           L+DG  +AA        L    + L  R+G+ ++E LD+     +    +Y+GG LDM  
Sbjct: 129 LRDGVAWAASRPADADDLHQYAEHLQTRYGYDRIEALDRDAFHALCPSPDYIGGTLDMGA 188

Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240
           GH+HPL LALG A A    G  I+E+S    I  G+   V T  G V A  +I+AGN YL
Sbjct: 189 GHLHPLRLALGLADAAAKAGARIHERSHVHDIRHGSKITVRTDAGHVIADQVILAGNGYL 248

Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300
           G L  ++ A+ MP    ++ATEPLG++    +L +D  V D  ++++Y+RL+ D RL+FG
Sbjct: 249 GGLDRQVIARVMPINNYIVATEPLGEDRM-KVLTRDVAVADSRFVVNYFRLSHDGRLLFG 307

Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360
           GG  YG R PA+I A++R +M   +P L+DV+IDYAW G   +T+ R+P + R+  N+  
Sbjct: 308 GGETYGYRFPADIPALVRKRMAVIYPHLRDVRIDYAWGGTLAITIRRMPYLARVRPNMLS 367

Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYG 420
           + G SGHGV     AGK+LAEA RG ++ F+ +  +PH PFPGG + RTP   +   ++ 
Sbjct: 368 ASGYSGHGVGTAIQAGKLLAEATRGTSDGFETYNAIPHTPFPGGGMFRTPLLTLAMTWFA 427

Query: 421 LRDKLG 426
           +RD+LG
Sbjct: 428 MRDRLG 433


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: 573
Number of extensions: 30
Number of successful extensions: 3
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: 434
Length adjustment: 32
Effective length of query: 395
Effective length of database: 402
Effective search space:   158790
Effective search space used:   158790
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.

Links

Downloads

Related tools

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