GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuB in Pseudomonas fluorescens FW300-N2E3

Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate AO353_29290 AO353_29290 gamma-glutamylputrescine oxidoreductase

Query= SwissProt::P37906
         (426 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_29290 AO353_29290
           gamma-glutamylputrescine oxidoreductase
          Length = 427

 Score =  618 bits (1593), Expect = 0.0
 Identities = 290/426 (68%), Positives = 349/426 (81%)

Query: 1   MTEHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASR 60
           M +H +SYYAA+ N+   F  L E + CDVCV+G GYTGLSSAL L+EAG+ V VLEA++
Sbjct: 2   MQKHVNSYYAATRNETIDFPVLEELVECDVCVIGAGYTGLSSALFLSEAGYSVTVLEAAK 61

Query: 61  IGFGASGRNGGQLVNSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCDY 120
           +G+GASGRNGGQLVNSYSRD+DVIE+ YG  TA +LGSM+FEG +IIR RIK+Y I CDY
Sbjct: 62  VGYGASGRNGGQLVNSYSRDVDVIEERYGDKTAEVLGSMIFEGADIIRSRIKQYDIKCDY 121

Query: 121 RPGGLFVAMNDKQLATLEEQKENWERYGNKQLELLDANAIRREVASDRYTGALLDHSGGH 180
           +PGG+F A+N KQL  L EQK +WERYGNK L +LDA  I+REV  D Y G LLD  GGH
Sbjct: 122 KPGGIFAALNKKQLKGLAEQKSSWERYGNKNLRMLDAAEIKREVGCDNYVGGLLDMQGGH 181

Query: 181 IHPLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNAYLGD 240
           IHPLNLA+GEA AI   GG++YE SA  +I +  P  VRTAKG V AKY+++AGNAYL  
Sbjct: 182 IHPLNLALGEAAAIIGLGGKIYEQSAAVEITYGEPITVRTAKGVVRAKYLLIAGNAYLPQ 241

Query: 241 KVEPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGG 300
            ++  + ++SMPCG+Q++ TE LS  +A+SLI  NYCVEDCNYLLDYYRLTADNRLLYGG
Sbjct: 242 DLDNRVTRKSMPCGSQIVVTEPLSAKVAKSLISNNYCVEDCNYLLDYYRLTADNRLLYGG 301

Query: 301 GVVYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNIYYM 360
           GVVYGAR+PDD+E+L+ PK+LKTFPQLK VKIDYRWTGNFLLT+SRMPQFGR++ N YYM
Sbjct: 302 GVVYGAREPDDIEQLIRPKILKTFPQLKDVKIDYRWTGNFLLTMSRMPQFGRIEKNAYYM 361

Query: 361 QGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAYYSL 420
           QGYSGHGVTC+HLAG+LI+E++RGDAERFDAFA+LPH P  GGRT + P TAMGAAYY+L
Sbjct: 362 QGYSGHGVTCSHLAGKLISEMIRGDAERFDAFASLPHMPMFGGRTFQAPLTAMGAAYYAL 421

Query: 421 RDRLGV 426
           RDR G+
Sbjct: 422 RDRFGI 427


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: 672
Number of extensions: 22
Number of successful extensions: 1
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: 427
Length adjustment: 32
Effective length of query: 394
Effective length of database: 395
Effective search space:   155630
Effective search space used:   155630
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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