GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lpd in Dinoroseobacter shibae DFL-12

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate 3606907 Dshi_0335 pyridine nucleotide-disulphide oxidoreductase dimerisation region (RefSeq)

Query= SwissProt::P11959
         (470 letters)



>lcl|FitnessBrowser__Dino:3606907 Dshi_0335 pyridine
           nucleotide-disulphide oxidoreductase dimerisation region
           (RefSeq)
          Length = 470

 Score =  220 bits (560), Expect = 9e-62
 Identities = 154/455 (33%), Positives = 238/455 (52%), Gaps = 18/455 (3%)

Query: 8   IETETLVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQ 67
           IET+  V+GAG GG   A  A Q+G +V ++E   +GG CLN GC+PSKALI+A  +   
Sbjct: 5   IETDICVIGAGSGGLSVAAGAVQMGARVVLIEGHLMGGDCLNFGCVPSKALIAAG-KQAH 63

Query: 68  AKHSEEMGIKAENVTIDFAKVQEWKASVVKKLTG-GVEGLLKGNKVEIVKGEAYFVDANT 126
              +   G+      ID+A  ++    V+  +     +   +G    +++  A F+    
Sbjct: 64  IVRAGGFGVAPAEPVIDYAAAKDHVRRVIDTIAPVDSQERFEGLGCTVIREYASFISETE 123

Query: 127 VRVVNGDSAQTYTFKNAIIATGSRPI--ELPNFKFSNRILDSTGALNLGEVPKSLVVIGG 184
           ++   GD+    T +  +IATGSRP    +P  +      + T   +L E P+ L++IGG
Sbjct: 124 LQA--GDT--VITARRFVIATGSRPFVPPIPGVEDVPYYTNET-IFDLREKPEHLIIIGG 178

Query: 185 GYIGIELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKGAE 244
           G IG+E+  A+   G KVT+LEGA + L   + ++AAI  +RL+ +G+E++  A A    
Sbjct: 179 GPIGMEMAQAHVRLGCKVTVLEGA-QALGKDDPELAAIALERLRGEGIEIIEGAQASNIS 237

Query: 245 EREDGVTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQCRT 304
            +   +TV   ANG++ T    ++L+ VGR PN D+L LE  G+    RGL +VD   RT
Sbjct: 238 GKGGAITVE-TANGQSVT--GTHLLMAVGRTPNLDKLNLEAAGVDYDRRGL-KVDASLRT 293

Query: 305 SVPNIFAIGDIVPGPALAHKASYE-GKVAAEAIAGHPSAVDYVAIPAVVFSDPECASVGY 363
           +   I+  GD+       H A Y  G +  + + G P+      +P   ++DPE A VG 
Sbjct: 294 TNKRIYGAGDVAGPLQFTHVAGYHAGILIRQLVLGLPAKTRDDHVPWATYTDPEIAQVGL 353

Query: 364 FEQQAKDE-GIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNASDM 422
            E QA+++ G  +  A+F +  N RA+A   T G +K++V K  G  IGA I+G  A ++
Sbjct: 354 TEAQAREKYGAALEVARFEYDENDRAIASGKTTGLIKVMVVK--GRPIGASIVGAEAGEL 411

Query: 423 IAELGLAIEAGMTAEDIALTIHAHPTLGEIAMEAA 457
           I     AI        +A  I  +PTLGEI   AA
Sbjct: 412 IGLWAYAIANKHKMSAVANMIAPYPTLGEINKRAA 446


Lambda     K      H
   0.316    0.135    0.376 

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: 545
Number of extensions: 35
Number of successful extensions: 11
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: 470
Length adjustment: 33
Effective length of query: 437
Effective length of database: 437
Effective search space:   190969
Effective search space used:   190969
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 (21.6 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