GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Pseudomonas stutzeri RCH2

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate GFF2185 Psest_2230 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes

Query= CharProtDB::CH_004665
         (470 letters)



>FitnessBrowser__psRCH2:GFF2185
          Length = 452

 Score =  240 bits (612), Expect = 8e-68
 Identities = 150/449 (33%), Positives = 235/449 (52%), Gaps = 20/449 (4%)

Query: 11  DTLVIGAGPGGYVAAIRAAQLGQKVTVVEKATLGGVCLNVGCIPSKALINAGHRYENAKH 70
           D  VIGAG GG  AA  AA  G +V V E   LGG C+NVGC+P K L+   H  E+   
Sbjct: 6   DLFVIGAGSGGVRAARFAAGFGARVAVAESRYLGGTCVNVGCVPKKLLVYGAHYAEDIGQ 65

Query: 71  SDDMGITAENVTVDFTKVQEWKASVVNKLTGGVAGLLKGNKVDVVKGEAYFVDSNSVRVM 130
           +   G T +  T D+ ++   K   + +L G    +L  + V +++  A  VD+++V V 
Sbjct: 66  AQGYGWTIDGATFDWNRLIANKDREIQRLNGIYRSILVDSGVTLLQAHARLVDAHTVEV- 124

Query: 131 DENSAQTYTFKNAIIATGSRPIELPNFKYSERVLNSTGALALKEIPKKLVVIGGGYIGTE 190
                + Y+ ++ +IATG  P  +P     E  + S  A  L+ +P++++V+GGGYI  E
Sbjct: 125 ---EGKRYSAEHILIATGGWP-HVPEIAGREHAITSNEAFYLESLPRRVLVVGGGYIAVE 180

Query: 191 LGTAYANFGTELVILEGGDEILPGFEKQMSSLVTRRLKKKGNVEIHTNAMAKGVEERPDG 250
             + +   G +  +L  G+  L GF+  +   +   + KKG V++  NA    ++++PDG
Sbjct: 181 FASIFHGCGADTKLLYRGELFLRGFDGSLRDHLKDEMIKKG-VDLQFNADIVHIDKQPDG 239

Query: 251 -VTVTFEVKGEEKTVDADYVLITVGRRPNTDELGLEQVGIEMTDRGIVKTDKQCRTNVPN 309
            +  T E   + +T++AD +    GRRP  D LGLEQ G+ +  RG +  D + RT+V +
Sbjct: 240 SLLATLE---DGRTLEADCIFYATGRRPMLDNLGLEQAGVALDARGFIAVDDEYRTSVSS 296

Query: 310 IYAIGDIIEGPPLAHKASYEGKIAAEAI--AGEPAEIDYLGIPAVVFSEPELASVGYTEA 367
           I AIGD+I    L   A  EG   A  +    +  ++DY  IP  VFS P +A+VG TE 
Sbjct: 297 ILAIGDVIGRIQLTPVALAEGMAVARRLFKPEQYRKVDYATIPTAVFSLPNMATVGLTEE 356

Query: 368 QAKEEGLDIVAAKFPFAANGRALSLNETD----GFMKLITRKEDGLVIGAQIAGASASDM 423
           +A+E+G  +      F +  R + L  TD      MKL+   E   V+G  +AG  A ++
Sbjct: 357 EAREKGYKVTI----FESRFRPMKLTMTDSLERSLMKLVVDAETDRVLGCHMAGPEAGEI 412

Query: 424 ISELSLAIEGGMTAEDIAMTIHAHPTLGE 452
           I  L++A++ G T +    T+  HPT  E
Sbjct: 413 IQGLAVALKAGATKQVFDETMGIHPTAAE 441


Lambda     K      H
   0.314    0.134    0.372 

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: 465
Number of extensions: 24
Number of successful extensions: 4
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: 470
Length of database: 452
Length adjustment: 33
Effective length of query: 437
Effective length of database: 419
Effective search space:   183103
Effective search space used:   183103
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 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