GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS13020 BPHYT_RS13020 mercuric
           reductase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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