GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Pseudomonas fluorescens FW300-N2E2

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate Pf6N2E2_4388 Gamma-glutamyl-putrescine oxidase (EC1.4.3.-)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4388
          Length = 437

 Score =  382 bits (981), Expect = e-110
 Identities = 200/419 (47%), Positives = 264/419 (63%), Gaps = 4/419 (0%)

Query: 9   SYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGAS 68
           SYYAAS+ P P  P LQ ++  DVCV+G G++GL++A+ L E G  V +LEA ++G+GAS
Sbjct: 17  SYYAASSLPQPDHPLLQGELLADVCVVGGGFSGLNTAIELAERGMSVVLLEAHRIGWGAS 76

Query: 69  GRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGVF 128
           GRNGGQ++      +D     +G    + +  M  E   I+R+RV ++QI CDL  G   
Sbjct: 77  GRNGGQLIRGVGHGLDQFAPIIGADGVRQMKLMGLEAVEIVRQRVERFQIPCDLTWGYCD 136

Query: 129 AALTAKQM-GHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHPLN 187
            A     + G  E  + L          LL    +  VV  + YVGG++DM  GH+HPLN
Sbjct: 137 LANKPSDLEGFAEDAEELRSLGYRHPTRLLQANEMHSVVGSDRYVGGLIDMGSGHLHPLN 196

Query: 188 LALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVPEL 247
           LALGEAAA + LG  ++EQS   RI+ G    VHT QG VRAK +++  NAYL  L P+L
Sbjct: 197 LALGEAAAAQQLGVRLFEQSAVTRIDYGPEVKVHTQQGSVRAKTLVLGCNAYLNGLNPQL 256

Query: 248 AAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVYGA 307
             K +P G+ +IATEPL    A +LLPQ+  V D    LDYYRL+ D+RL+FGG   Y  
Sbjct: 257 GGKVLPAGSYIIATEPLSQAQAQALLPQNMAVCDQRVALDYYRLSADRRLLFGGACHYSG 316

Query: 308 RDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NIYYSQGCS 365
           RDP +I A +RPKMLK FPQL DVKIDY W G   +  +RLPQ+GRL D  N+YY+Q  S
Sbjct: 317 RDPQDIGAYMRPKMLKVFPQLADVKIDYQWGGMIGIGANRLPQIGRLKDQPNVYYAQAYS 376

Query: 366 GHGVTYTHLAGKVLAEALRGQ-AERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 423
           GHGV  THLAGK+LAEA+ GQ +  FD FA +PH  FPGG+ LR+P  A+G  ++ L++
Sbjct: 377 GHGVNATHLAGKLLAEAISGQHSSGFDLFAQVPHMTFPGGKHLRSPLLALGMLWHRLKE 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: 617
Number of extensions: 35
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: 437
Length adjustment: 32
Effective length of query: 395
Effective length of database: 405
Effective search space:   159975
Effective search space used:   159975
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