GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF2185 Psest_2230
           Pyruvate/2-oxoglutarate dehydrogenase complex,
           dihydrolipoamide dehydrogenase (E3) component, and
           related enzymes
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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