GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Klebsiella michiganensis M5al

Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate BWI76_RS10690 BWI76_RS10690 gamma-glutamylputrescine oxidoreductase

Query= SwissProt::P37906
         (426 letters)



>FitnessBrowser__Koxy:BWI76_RS10690
          Length = 426

 Score =  778 bits (2010), Expect = 0.0
 Identities = 376/426 (88%), Positives = 403/426 (94%)

Query: 1   MTEHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASR 60
           M+EHT+SYYAASAN+Y PF TL ESI+CDVCVVGGGYTGLSSALHLAE G+DVV+LE +R
Sbjct: 1   MSEHTTSYYAASANRYEPFPTLGESISCDVCVVGGGYTGLSSALHLAEMGYDVVLLEGAR 60

Query: 61  IGFGASGRNGGQLVNSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCDY 120
           IGFGASGRNGGQLVNSYSRDIDVIEK+YG D A+MLGSMMFEGG+IIRERI+RYQI CDY
Sbjct: 61  IGFGASGRNGGQLVNSYSRDIDVIEKTYGPDAAKMLGSMMFEGGDIIRERIQRYQIQCDY 120

Query: 121 RPGGLFVAMNDKQLATLEEQKENWERYGNKQLELLDANAIRREVASDRYTGALLDHSGGH 180
           RPGGLFVA+N KQL TLEEQK NWERYGN QLELLDA+AIRREV SDRY GALLDHSGGH
Sbjct: 121 RPGGLFVALNHKQLETLEEQKANWERYGNTQLELLDASAIRREVDSDRYAGALLDHSGGH 180

Query: 181 IHPLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNAYLGD 240
           IHPLNLAIGEADAIRLNGGRVYE S VT+IQH++PAVV T +GQVTA+YVIVAGNAYLGD
Sbjct: 181 IHPLNLAIGEADAIRLNGGRVYEQSPVTRIQHSSPAVVTTERGQVTARYVIVAGNAYLGD 240

Query: 241 KVEPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGG 300
           K+EPELAKRSMPCGTQV+ T  L+EDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGG
Sbjct: 241 KLEPELAKRSMPCGTQVVATAPLAEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGG 300

Query: 301 GVVYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNIYYM 360
           GVVYGARDPDDVERL++PKLLKTFPQL+GVKIDYRWTGNFLLTLSRMPQFGRLD NIYYM
Sbjct: 301 GVVYGARDPDDVERLIMPKLLKTFPQLQGVKIDYRWTGNFLLTLSRMPQFGRLDNNIYYM 360

Query: 361 QGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAYYSL 420
           QGYSGHGVTCTHLAGRLI+ELLRGDAERFDAFA LPHYPFPGGR+LR+PFTAMGAAYYSL
Sbjct: 361 QGYSGHGVTCTHLAGRLISELLRGDAERFDAFAKLPHYPFPGGRSLRIPFTAMGAAYYSL 420

Query: 421 RDRLGV 426
           RDRLGV
Sbjct: 421 RDRLGV 426


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: 791
Number of extensions: 14
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: 426
Length adjustment: 32
Effective length of query: 394
Effective length of database: 394
Effective search space:   155236
Effective search space used:   155236
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