GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS10690 BWI76_RS10690
           gamma-glutamylputrescine oxidoreductase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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