GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuB in Amantichitinum ursilacus IGB-41

Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate WP_053938621.1 WG78_RS14815 FAD-binding oxidoreductase

Query= SwissProt::P37906
         (426 letters)



>NCBI__GCF_001294205.1:WP_053938621.1
          Length = 428

 Score =  344 bits (882), Expect = 3e-99
 Identities = 178/422 (42%), Positives = 265/422 (62%), Gaps = 2/422 (0%)

Query: 2   TEHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRI 61
           TEH +S+YAA+AN       L  ++ CDV VVG G TGL +AL+LAE G+ VVVLEA+R+
Sbjct: 6   TEHIASWYAATANDSTRHAPLMGTLACDVLVVGAGLTGLHAALNLAERGYKVVVLEAARV 65

Query: 62  GFGASGRNGGQLVNSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCDYR 121
           G+ ASGRNGGQ++N ++  +D  E     +  + +  M  E   ++RERI ++ IDCDYR
Sbjct: 66  GWAASGRNGGQVINGFACGMDTFESELPKEDLQRVFDMGIEANTLLRERIAKHNIDCDYR 125

Query: 122 PGGLFVAMNDKQLATLEEQK-ENWERYGNKQLELLDANAIRREVASDRYTGALLDHSGGH 180
            G L  A     +  L+  + E  +R+G   L  ++ + +   V S+RY G L D + GH
Sbjct: 126 AGYLTAANKAAHVKDLQAWRDEAAQRWGYPDLSWVERSELPGYVQSERYAGGLFDPNSGH 185

Query: 181 IHPLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNAYLGD 240
           +HPLN  +G A A    G +++E S VT++Q  TP V++TA GQV A++V++A NA++ +
Sbjct: 186 LHPLNYTLGLARAAVAAGVQIFEHSLVTEMQQGTPHVLKTAHGQVQAQFVVLACNAFI-E 244

Query: 241 KVEPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGG 300
            + P L ++ MP GT VITTE ++    ++L+P    + D  ++LDY+R T D R+L+GG
Sbjct: 245 HLSPALNRKIMPVGTYVITTEPITPVRFKALMPAGAAICDSRFVLDYFRPTPDGRVLWGG 304

Query: 301 GVVYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNIYYM 360
            V Y    P ++ + +   +LKTFPQL  +KI + W G   +T++R P FGRL + +Y+ 
Sbjct: 305 KVSYSTLAPANLAQAMRADMLKTFPQLADIKIIHAWGGMVDITMNRAPHFGRLASTVYFA 364

Query: 361 QGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAYYSL 420
           QG+SGHGV  + LAG+L+AE + G AERFD F  + H+ FPGG  LR P   +  A+Y L
Sbjct: 365 QGFSGHGVNVSGLAGKLMAEAIAGQAERFDIFTKIRHHDFPGGDLLRTPSLVLAMAWYRL 424

Query: 421 RD 422
           +D
Sbjct: 425 KD 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: 470
Number of extensions: 27
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: 428
Length adjustment: 32
Effective length of query: 394
Effective length of database: 396
Effective search space:   156024
Effective search space used:   156024
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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