GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3606907
          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.

Links

Downloads

Related tools

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