GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Shewanella oneidensis MR-1

Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate 200442 SO1264 hypothetical oxidoreductase (NCBI ptt file)

Query= SwissProt::P37906
         (426 letters)



>FitnessBrowser__MR1:200442
          Length = 435

 Score =  348 bits (894), Expect = e-100
 Identities = 175/423 (41%), Positives = 259/423 (61%), Gaps = 3/423 (0%)

Query: 3   EHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIG 62
           ++  SYY  +A +      L  SIT DVC+VGGG++G+++A+ L + G  VV+LEA R+G
Sbjct: 11  QYPHSYYLDTAKEIYAHPQLEGSITADVCIVGGGFSGINTAIELRQRGLSVVLLEAKRMG 70

Query: 63  FGASGRNGGQLVNSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCDYRP 122
           +GASGRNGG+L+     D        G +    +  M FE  +I+R RI+ +QIDCD + 
Sbjct: 71  WGASGRNGGELIRGIGHDPAQFINEIGQEGVSAIQQMGFEAVDIVRNRIQTHQIDCDLQM 130

Query: 123 GGLFVAMNDKQLATLEEQKENWERYGNK-QLELLDANAIRREVASDRYTGALLDHSGGHI 181
           G   +A+  + +  L+E+ E+ +  G K +++LL  + +   + SD Y GAL+D   GH+
Sbjct: 131 GYCDLAVKPRHMIELQEEFESLKSLGYKHEIKLLAQSQLGNVIGSDFYQGALVDMGSGHL 190

Query: 182 HPLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNAYLGDK 241
           HPLNLA+GEA   R  G +++E SA  +I       V TAKG+VT +Y+++AGNAY+G K
Sbjct: 191 HPLNLALGEARVARELGAQLFEYSAAEKIIQGDKPKVLTAKGEVTCQYLVLAGNAYIGHK 250

Query: 242 VEPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGGG 301
           +   +  + +P G+ ++ TE L++   +++IP+N    D    LDY+ L+AD RLL+GG 
Sbjct: 251 LNSYIGGKVLPAGSYLLATEPLTQQQCKNIIPQNMAFADMRIALDYFHLSADRRLLFGGL 310

Query: 302 VVYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLD--TNIYY 359
             Y  +DP D+E  + P L K FPQLKGV+IDY W G   +  +RMPQ GRL   +NI++
Sbjct: 311 CTYSGKDPKDIEAALRPNLEKVFPQLKGVRIDYEWGGMIGIGANRMPQIGRLPDASNIFF 370

Query: 360 MQGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAYYS 419
            Q Y+GHGV  TH+A +L+AE +   A  FD FA + H  FPGG T R P  A G  Y+ 
Sbjct: 371 AQAYAGHGVNATHMAAKLLAEAICQQAGHFDVFAKIKHMTFPGGPTFRSPMLAAGMLYHR 430

Query: 420 LRD 422
            +D
Sbjct: 431 FKD 433


Lambda     K      H
   0.320    0.138    0.411 

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: 510
Number of extensions: 22
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: 426
Length of database: 435
Length adjustment: 32
Effective length of query: 394
Effective length of database: 403
Effective search space:   158782
Effective search space used:   158782
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