GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Herbaspirillum seropedicae SmR1

Align 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)
to candidate HSERO_RS19055 HSERO_RS19055 oxidoreductase

Query= SwissProt::O18404
         (255 letters)



>FitnessBrowser__HerbieS:HSERO_RS19055
          Length = 256

 Score =  116 bits (290), Expect = 5e-31
 Identities = 82/250 (32%), Positives = 138/250 (55%), Gaps = 19/250 (7%)

Query: 6   VSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKEL---GDKVVFVPVDVTSE 62
           V+LVTGGA G+G + +++LA +G +V++AD+     ++ A  L   G +   + +D+ S 
Sbjct: 10  VALVTGGAMGIGASISQQLAAKGHTVLVADINLDAASKTADALVAAGHRAAPLQMDLGSP 69

Query: 63  KDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGTFNV 122
           + ++AA    +  +GR D+ VN AG A   +T++F   + + LE++ + +N+N  G    
Sbjct: 70  ESIAAAFAHIEKDYGRCDVLVNNAGVA---RTYSF---LDYPLENWLQTMNVNVTGVLLA 123

Query: 123 IRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDLST 182
            + +A LM         Q G IVN +S++      G+ AY  SKAAV+G+T  +A +L+ 
Sbjct: 124 GQHAARLMVKQ------QWGRIVNISSISGIRAGAGRTAYGTSKAAVIGLTRQMAIELAQ 177

Query: 183 QGIRICTIAPGLFNTPMLAAL-PEKVRTFLAKSIPFPQRLGEPSEYAHLV--QAIYENPL 239
            GI + ++APG  +TPM  A+  E+ R    + +P  +R G   E A  V   A  E+  
Sbjct: 178 YGITVNSVAPGPVDTPMTQAMHSEQTRESYYRLVPM-RRYGTTDEIASAVCYLAAEESAY 236

Query: 240 LNGEVIRIDG 249
           + G VI +DG
Sbjct: 237 ITGHVIPVDG 246


Lambda     K      H
   0.317    0.133    0.369 

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: 129
Number of extensions: 7
Number of successful extensions: 2
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: 255
Length of database: 256
Length adjustment: 24
Effective length of query: 231
Effective length of database: 232
Effective search space:    53592
Effective search space used:    53592
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: 47 (22.7 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