GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Desulfovibrio vulgaris Hildenborough

Align decanoate oxidase (EC 1.3.3.6; EC 5.3.3.14) (characterized)
to candidate 207537 DVU2064 oxidoreductase, 2-nitropropane dioxygenase family

Query= metacyc::HP0773-MONOMER
         (363 letters)



>MicrobesOnline__882:207537
          Length = 373

 Score =  254 bits (649), Expect = 3e-72
 Identities = 147/366 (40%), Positives = 211/366 (57%), Gaps = 28/366 (7%)

Query: 8   LKIGKHTIKFPIFQGGMGVGISWDELAGNVAKEGALGVISAVGTGYYKNMRFVERIVAKK 67
           L+IG    + PI QGGMGVGIS   LA  VA EG +GVI+    G        E  VAK 
Sbjct: 6   LQIGDLVARVPIIQGGMGVGISLSRLASAVANEGGIGVIAGAMIG------MKEPDVAKN 59

Query: 68  PFEALNFYSKKALNEIFANARKICGNNPLGANILYAINDYGRVLRDSCEAGANIIITGAG 127
           P EA    + +AL      A +      +G NI+ A+  +  ++R S E+ A+II +GAG
Sbjct: 60  PIEA----NLRALRREIEKAHEAT-KGIVGVNIMVALTTFSEMVRTSIESRADIIFSGAG 114

Query: 128 LPTNMPEFAKDFSD-------VALIPIISSAKALKILCKRWSDRYKRIPDAFIVEGPLSG 180
           LP ++P    D  +         L+PI+SSA+A  ++ K+W  R+  +PDAF+VEGP +G
Sbjct: 115 LPLDLPRHLHDACEQKKEEFRTKLVPIVSSARAASVIAKKWLSRFDYLPDAFVVEGPKAG 174

Query: 181 GHQGFKYEDCFKEEFRLENLVPKVVEASKEWGN-----IPIIAAGGIWDRKDIDTMLSLG 235
           GH GFK E+       LE++VP+V+EA K + +     +P+IAAGG++   DI   + +G
Sbjct: 175 GHLGFKPEEIDDPGHSLEHVVPEVIEAVKPFEDAKGRAVPVIAAGGVYSGDDIRRFIEMG 234

Query: 236 ASGVQMATRFLGTKECDA-KVYADLLPTLKKEDILLIKSPVGYPARAINTGVIKRIEEGN 294
           A+GVQM TRF+ T ECDA + +       ++ED+ +IKSPVG P RAI  G I+ + EG 
Sbjct: 235 AAGVQMGTRFVATHECDADERFKQAYVAAREEDVTIIKSPVGMPGRAIGNGFIEAMREGA 294

Query: 295 APKIACVSNCVAPCNRGEEAKKVGYCIADGLGRSYLGNREEGLYFTGANGYRVDKIISVH 354
                CV  C++ C    E ++  YCIA  L  +  GN E+G  F+G+N +R+D I+SV 
Sbjct: 295 KKPFKCVFKCISTC----EQEQTPYCIAAALINAMKGNLEKGFAFSGSNVFRIDSILSVR 350

Query: 355 ELIKEL 360
           +LI  L
Sbjct: 351 DLIGSL 356


Lambda     K      H
   0.319    0.139    0.418 

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: 385
Number of extensions: 25
Number of successful extensions: 6
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: 363
Length of database: 373
Length adjustment: 30
Effective length of query: 333
Effective length of database: 343
Effective search space:   114219
Effective search space used:   114219
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 (21.7 bits)
S2: 49 (23.5 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