GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Burkholderia phytofirmans PsJN

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate BPHYT_RS13020 BPHYT_RS13020 mercuric reductase

Query= SwissProt::P11959
         (470 letters)



>FitnessBrowser__BFirm:BPHYT_RS13020
          Length = 466

 Score =  229 bits (584), Expect = 1e-64
 Identities = 142/452 (31%), Positives = 231/452 (51%), Gaps = 13/452 (2%)

Query: 11  ETLVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQAKH 70
           + +V+G G GG   A+R A+ G++  ++E+   GG C+NVGC P+K+ ++++     A+H
Sbjct: 6   DAVVIGTGQGGSPLAVRLAKSGRETAVIERAAFGGTCVNVGCTPTKSYVASARAAHVARH 65

Query: 71  SEEMGIKAEN-VTIDFAKVQEWKASVVKKLTGGVEGLLKGNK-VEIVKGEAYFVDANTVR 128
             E+G++    +++D A V+  K  ++ +   GVE  L+G + + + KG A F     + 
Sbjct: 66  CAELGVQVGGAISVDLAAVKARKDKIIGQSRDGVEAWLRGTQNMSVFKGHARFTGPRALA 125

Query: 129 VV--NGDSAQTYTFKNAIIATGSRPIELPNFKFSN-RILDSTGALNLGEVPKSLVVIGGG 185
           +   +G+     +     I TG+R +  P       R   ++  L+L E+P  LV++G  
Sbjct: 126 ISGPDGNLLDEISADEVFINTGTRAVVPPLDGLERIRYYTNSNLLDLTELPSHLVIVGAS 185

Query: 186 YIGIELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKGAE- 244
           YI +E    +  FG++VT+L     +L+  +   A  ++K L ++GVE   N      E 
Sbjct: 186 YIALEFAQIFRRFGSQVTVLVRGERLLTREDADFADSVQKVLAREGVEFRFNVQPSRVEP 245

Query: 245 --EREDGVTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQC 302
              RE+ V V +E N     ++A ++L   GR PNTD+LGL   GI +   G I VD Q 
Sbjct: 246 HPHRENEVCVGFEQN--IPALEASHLLFATGREPNTDDLGLAAAGIAVDKHGTIPVDGQL 303

Query: 303 RTSVPNIFAIGDIVPGPALAHKASYEGK--VAAEAIAGHPSAVDYVAIPAVVFSDPECAS 360
           RT+VP ++AIGD+    A  H  SY+    VAA  + G   +VD   +   VF DP  A 
Sbjct: 304 RTNVPGVWAIGDVNGRGAFTH-TSYDDYQIVAANLLDGASRSVDTRIMAYAVFVDPPLAR 362

Query: 361 VGYFEQQAKDEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNAS 420
           VG  E + +  G D + A  P    GRA    +TDGF+K++V KE   ++GA I G    
Sbjct: 363 VGASEAEVRKSGRDALIATMPMTRVGRARERGETDGFMKVMVDKESKRVLGAAIHGIEGD 422

Query: 421 DMIAELGLAIEAGMTAEDIALTIHAHPTLGEI 452
           + +      + A      +   +H HPT+ E+
Sbjct: 423 EALHTFIDIMTADAPYPTLQYAMHIHPTISEL 454


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: 495
Number of extensions: 23
Number of successful extensions: 5
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: 466
Length adjustment: 33
Effective length of query: 437
Effective length of database: 433
Effective search space:   189221
Effective search space used:   189221
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:

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