GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF1136
          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.

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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