GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Pseudomonas simiae WCS417

Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate GFF5415 PS417_27720 FAD-dependent oxidoreductase

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



>FitnessBrowser__WCS417:GFF5415
          Length = 430

 Score =  385 bits (990), Expect = e-111
 Identities = 199/428 (46%), Positives = 275/428 (64%), Gaps = 4/428 (0%)

Query: 2   ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61
           A+  +  SYYAAS+   P  P L  D+  DVCV+G G++GL++AL L E GF V +LEA 
Sbjct: 3   ASARHTPSYYAASSVAQPDYPVLTGDMTADVCVVGGGFSGLNTALELAERGFSVVLLEAR 62

Query: 62  KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121
           K+ +GASGRNGGQ++      +D     +G +  + +  M  E   I+RERV ++QI CD
Sbjct: 63  KIAWGASGRNGGQLIRGVGHGLDQFANVIGTEGVRQMKLMGLEAVEIVRERVERFQIPCD 122

Query: 122 LKDGGVFAALTAKQMGHLESQKRLWERFGHT-QLELLDQRRIREVVACEEYVGGMLDMSG 180
           L  G    A  ++ +  L          G+  ++ LL   ++  V+  + YVGGM+DM  
Sbjct: 123 LTWGYCDLANKSRDLQGLAEDAEELRGLGYRHEVRLLHADQMSSVIGSDRYVGGMIDMGS 182

Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240
           GH+HPLNLALGEAAA + LG  ++EQS   RI+ G    VHT QG VRAK +++A NAYL
Sbjct: 183 GHLHPLNLALGEAAAAQQLGVKLFEQSEVTRIDYGPEVNVHTAQGNVRAKTLVLACNAYL 242

Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300
            +L P L+ K +P G+ +IATEPL +  A  LLPQ+  V D    +DY+RL+ D+RL+FG
Sbjct: 243 NDLNPRLSGKVLPAGSYIIATEPLSEAQAVDLLPQNMAVCDQRVTVDYFRLSADRRLLFG 302

Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NI 358
           G   Y  RDP +I A +RPKML+ FPQL DVKIDY W G   +  +RLPQ+GRL D  N+
Sbjct: 303 GACHYSGRDPKDIGAYMRPKMLQVFPQLADVKIDYQWGGMIGIGANRLPQIGRLTDQPNV 362

Query: 359 YYSQGCSGHGVTYTHLAGKVLAEALRGQAE-RFDAFADLPHYPFPGGQLLRTPFAAMGAW 417
           YY+Q  +GHG+  THLAGK+LAEA+ GQ + RFD FA +PH  FPGG+ LR+P  A+G  
Sbjct: 363 YYAQAYAGHGLNATHLAGKLLAEAISGQQQGRFDLFAQVPHITFPGGKHLRSPLLALGML 422

Query: 418 YYGLRDKL 425
           ++ L++++
Sbjct: 423 WHRLKERM 430


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: 599
Number of extensions: 28
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: 430
Length adjustment: 32
Effective length of query: 395
Effective length of database: 398
Effective search space:   157210
Effective search space used:   157210
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