GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_29290
          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 (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