GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Dechlorosoma suillum PS

Align decanoate oxidase (EC 1.3.3.6; EC 5.3.3.14) (characterized)
to candidate Dsui_1637 Dsui_1637 2-nitropropane dioxygenase-like enzyme

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



>FitnessBrowser__PS:Dsui_1637
          Length = 387

 Score =  179 bits (454), Expect = 1e-49
 Identities = 128/377 (33%), Positives = 197/377 (52%), Gaps = 23/377 (6%)

Query: 7   PLKIGKHTIKFPIFQGGMGVGISWDELAGNVAKEGALGVISAVGTGYYKNMRFVERIVAK 66
           PLKI   T+  PI QGGMGVGIS   LAG VA    +G I++V    +      E   ++
Sbjct: 8   PLKIKGKTL-VPIVQGGMGVGISAHRLAGTVASLNGVGTIASVDLRRHHPDLMAETGRSR 66

Query: 67  KPFEALNFYSKKALNEIFANARKIC-GNNPLGANILYAINDYGRVLRDSCEAGANIIITG 125
              EA+   +  AL+     A+ I  G   +  N++ A+  Y   +R SC++GA  I+ G
Sbjct: 67  NR-EAIEKANLIALDREIKMAQDIAQGRGVIAVNVMRAVTQYQDYVRQSCQSGAEAIVMG 125

Query: 126 AGLPTNMPEFAKDFSDVALIPIISSAKALKILCKRWSDRYKRIPDAFIVEGP-LSGGHQG 184
           AGLP ++PE  + + DVAL+PI+S  + + +L K+W  R  R+PDA ++E P  +GGH G
Sbjct: 126 AGLPLDLPELTEGYPDVALVPILSDVRGIVLLLKKWM-RKNRLPDAIVIEHPRYAGGHLG 184

Query: 185 -FKYEDCFKEEFRLENLVPKVVEASKEWG----NIPIIAAGGIWDRKDIDTMLSLGASGV 239
             K ED     F  E ++P V+EA +E G     IP+I AGGI   + +  ++ +GA+ V
Sbjct: 185 AAKKEDVNDPRFNFEVVIPGVLEAFEEMGIASEKIPLIPAGGINSHERVRELIDMGAAAV 244

Query: 240 QMATRFLGTKECDAKV-YADLLPTLKKEDILLIKSPVGYPARAINTGVIKRI---EE--- 292
           Q+ + F   +E DA + +  +L   K +D++   S  G PARA+ T  +++    EE   
Sbjct: 245 QLGSAFAVAEEGDADIEFKKVLAGAKDKDVVDFMSCAGLPARAVKTPWLEKYLNREEKLM 304

Query: 293 ----GNAPKIACVSNCVAPCNRGEEAKKVG-YCIADGLGRSYLGNREEGLYFTGANGYRV 347
               G   K     +C+  C   +   K G +CI + L  +  G+ ++GL+F GA+    
Sbjct: 305 AAAAGKEHKCTLAWDCLLQCGLRDSNPKHGQFCIDNQLAAAVTGDVQKGLFFRGASSLPF 364

Query: 348 DKII-SVHELIKELTEG 363
              I  V EL+  L  G
Sbjct: 365 GSAIRPVRELMHYLLTG 381


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: 338
Number of extensions: 18
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 363
Length of database: 387
Length adjustment: 30
Effective length of query: 333
Effective length of database: 357
Effective search space:   118881
Effective search space used:   118881
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: 50 (23.9 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