Aligments for a candidate for puuB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for puuB in Phaeobacter inhibens BS107

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate GFF1136 PGA1_c11510 gamma-glutamylputrescine oxidoreductase PuuB

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



>lcl|FitnessBrowser__Phaeo:GFF1136 PGA1_c11510
           gamma-glutamylputrescine oxidoreductase PuuB
          Length = 436

 Score =  335 bits (860), Expect = 1e-96
 Identities = 182/423 (43%), Positives = 257/423 (60%), Gaps = 4/423 (0%)

Query: 6   YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65
           YP S+YAA+A P+ P   LQ +   DVC++G GYTGLS+AL L E G  V +LEA +VGF
Sbjct: 15  YPNSWYAATATPLAPFAPLQGEARADVCIVGGGYTGLSAALHLAEAGRSVILLEANRVGF 74

Query: 66  GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125
           GASGRNGGQ+ +    + D +E  +G   A  L ++A +   +++  +A++ I C LK G
Sbjct: 75  GASGRNGGQLGSGQRMEQDGLESLMGEPDAAKLWHLAEDAKDLVKSLIARHDIDCHLKPG 134

Query: 126 GVFAALTAKQMGHLESQ-KRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIH 184
              A  +   + H     + L  R+G+  +  LD+  ++ +     YVGG LDM  GH+H
Sbjct: 135 IAHACFSKSDVSHEHRYVEHLQTRYGYGDITALDKAALQAICPSPAYVGGSLDMGAGHLH 194

Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244
           PL  ALG A A  + G  I E S  + IE GA   + T +G+V A  +I+A N YLG L 
Sbjct: 195 PLAYALGLARAAAAAGVQICEGSEVLDIEDGAQIRLRTAEGQVTADHLILACNGYLGGLN 254

Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304
            ++AA+ MP    + ATEPLG + A  +L +D  V D  ++++Y+RL+ D RL+FGGG  
Sbjct: 255 RQVAARVMPINNFIAATEPLGADAAQ-VLARDVAVADSKFVVNYFRLSHDGRLLFGGGES 313

Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGC 364
           YG R P++I A +R  M + FP L+DVKIDYAW G   +TL R+P + RLG NI  + G 
Sbjct: 314 YGYRFPSDIAATVRKPMTEIFPHLRDVKIDYAWGGTLAITLKRMPYLARLGPNILSASGY 373

Query: 365 SGHGV-TYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 423
           SGHGV T TH AG+++A A+ G  + FD  A +P   FPGG  +R+P  A+   +Y LRD
Sbjct: 374 SGHGVGTATH-AGQLMALAVAGDGDGFDTMARVPAPAFPGGAAMRSPLLALAMTWYALRD 432

Query: 424 KLG 426
           +LG
Sbjct: 433 RLG 435


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: 32
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: 436
Length adjustment: 32
Effective length of query: 395
Effective length of database: 404
Effective search space:   159580
Effective search space used:   159580
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources