GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puo in Nocardioides daejeonensis MJ31

Align Putrescine oxidase; EC 1.4.3.10 (uncharacterized)
to candidate WP_110206665.1 DNK54_RS09145 FAD-dependent oxidoreductase

Query= curated2:P40974
         (478 letters)



>NCBI__GCF_003194585.1:WP_110206665.1
          Length = 500

 Score =  226 bits (575), Expect = 2e-63
 Identities = 152/460 (33%), Positives = 227/460 (49%), Gaps = 21/460 (4%)

Query: 16  DVVVVGAGPAGLMAARTLVAAGRTVAVLEARDRVGGRTWSKTV-DGAFLEIGGQWISPDQ 74
           DVVVVG G +GL+AAR L     +V V+EAR RVGGR  +  +  G  +E GG ++ P Q
Sbjct: 50  DVVVVGGGLSGLVAARRLARTKHSVLVVEARKRVGGRLLNHDLRTGGTIEAGGAFVGPTQ 109

Query: 75  TELLALVDELGLETYQRYREGESVYLAPDGTRHTYTGSMFPAGESTIVEMEKLVALLDGL 134
             +  L  +LG+ T+  Y  G++VYL+    R+ +TG++ P   + +++    +  LD  
Sbjct: 110 NHIKRLAAQLGVRTFDEYVAGKNVYLSSTLGRNEFTGTI-PPDPTILLDAAIALGQLDQY 168

Query: 135 VAEIGATEPWAHPAARELDTISFHHWLRQHSDDEAACSN-IGIFVAGGMLTKPAHAFSVL 193
            A +    PW HP A   D ++   W+R+++ ++A  SN I  +        P     + 
Sbjct: 169 AASMPVDAPWTHPQAAAWDAMTLGDWIRRNTINKAGISNLIKAWTQPTFGADPDQLSFLF 228

Query: 194 QAVLMAASA-----GSFSNLVDE-DFILDRRVVGGMQSVSETMAAELGEDVVFLDTPVRT 247
               +A S      G+F+   D      + R VGG Q +   +A +LG  V  L   VR 
Sbjct: 229 VIHYLACSGDERTPGTFARSSDTAGGAQESRFVGGSQRIPLLLAKQLGRRVA-LGAAVRR 287

Query: 248 IRWAGDGGTYAEHVPGTPVTVWSDRLTVRAKDVVVAVPPNLYSRISFEPPLPRLQHQMHQ 307
           I          EH  G+ V V + R TV A+ V+VA PP     I F P LP  +  + +
Sbjct: 288 I----------EH-HGSRVRVHTARGTVSARRVIVAAPPEQVLGIDFSPGLPTGRRALLR 336

Query: 308 HQSLGLVIKVHAVYETPFWRDKGLSGTGFGAHELSQEVYDNTNHGDPRGTLVGFVSDERA 367
              +G ++K  AVYE PFWR+ GLSG G       +  +DN   G   G L+ FV     
Sbjct: 337 RLEMGQLMKCDAVYEKPFWREAGLSGFGIADSGAVRAAFDNGVPGTDHGILLAFVGGSTW 396

Query: 368 DELFGLPAEERRRLILESLSHYLGEEALHPVVYYESDFGSEEWTRGAYAASYDLGGLHRY 427
            E   +    RR+ +L+  +   G++AL P+ Y E D+  E WT G   A Y  G + R+
Sbjct: 397 REFGPMSRARRRKAVLQGFAAMFGDQALRPIEYTEQDWTKERWTGGGPVAIYGPGVMARF 456

Query: 428 GAHQRTPVGPIRWACSDLAAEGYQHVDGALRQGRLAAAEV 467
           G H RTP   + WA ++ +     ++DGA+R G  AA EV
Sbjct: 457 GQHIRTPYRRVHWAGTETSTYWTGYMDGAVRAGERAALEV 496


Lambda     K      H
   0.318    0.135    0.406 

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: 739
Number of extensions: 41
Number of successful extensions: 5
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: 478
Length of database: 500
Length adjustment: 34
Effective length of query: 444
Effective length of database: 466
Effective search space:   206904
Effective search space used:   206904
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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