GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Sphingomonas koreensis DSMZ 15582

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate Ga0059261_1239 Ga0059261_1239 mercury(II) reductase

Query= SwissProt::P85207
         (461 letters)



>FitnessBrowser__Korea:Ga0059261_1239
          Length = 479

 Score =  256 bits (653), Expect = 1e-72
 Identities = 175/462 (37%), Positives = 242/462 (52%), Gaps = 16/462 (3%)

Query: 2   KTYDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHH 61
           K YDLIV+G G  G+ AAI  A+ G +V  + A  +GG C+NVGC+P+KAL+ A E++HH
Sbjct: 14  KKYDLIVVGGGSAGFSAAITAAEQGAQVAVIGAGTIGGTCVNVGCVPSKALIRAVESIHH 73

Query: 62  LKGA----EGFGLKAKPELDLKKLGAWRDGVVKKLTGG-VAGLLK-GNKVELLRGFARFK 115
              A    +G   +A+   D  ++ A +D +V  L     A LL   N V    G AR  
Sbjct: 74  ANAAPMRFKGIEARARAA-DWGQVIAEKDALVSGLRQAKYADLLPLYNNVAYHEGTARLV 132

Query: 116 GPREIEVNGETYGAQSFIIATGSEPM--PLKGFPFGEDVWDSTRALRVEEGIPKRLLVIG 173
               +E  G  + A   +IATG+ P    + G P   D  DST AL + E +PK ++V+G
Sbjct: 133 D-NGVETGGRRFTADRIVIATGTRPAVPAIPGLP-DVDALDSTTALDLTE-LPKSMIVLG 189

Query: 174 GGAVGLELGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGY 233
           GG VG+EL Q + R G +VTL+ +   +LP  + E  A L   L  EG+ V         
Sbjct: 190 GGYVGVELAQTFSRAGVDVTLV-FRSRLLPEMEPEIGAALTDYLSSEGITVLGNLAYQSV 248

Query: 234 EKKQDGLHVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNAR 293
            K  +G    L   + G  E IV +++L+A GR P  E LGL +AGVK    G I V+  
Sbjct: 249 HKTAEG-GAALTVLRDGVAEIIVAERLLLATGRAPNVEDLGLIEAGVKQTLSGAIIVDDH 307

Query: 294 METSAPGVYAIGDVARPPLLAHKAMKEGLVAAENAAGKNALF--DFQVPSVVYTGPEWAG 351
           M TS  GVYA GDV       + A     +AA+NA   ++L   +  +PSVV++ P+ A 
Sbjct: 308 MRTSVRGVYAAGDVTGRDQFVYMAAYGAKIAAKNALNGDSLRYDNSAMPSVVFSDPQVAS 367

Query: 352 VGLTEEEARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAG 411
           VG TE +A  AGY  +    P     RAL      GLIK+V D  T  LLG  ++ P+  
Sbjct: 368 VGFTEAQAIAAGYAARTSTLPLENVPRALAARDTRGLIKLVADGRTRKLLGAHILAPEGA 427

Query: 412 ELIAEATLALEMGATVSDLGLTIHPHPTLSEGLMEAAEALHK 453
           + I  A +AL  G T+ DL  TI P+ T  EGL  AA+A  +
Sbjct: 428 DSIQTAAMALRCGLTIDDLVETIFPYLTTVEGLKLAAQAFDR 469


Lambda     K      H
   0.316    0.138    0.395 

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: 31
Number of successful extensions: 6
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: 461
Length of database: 479
Length adjustment: 33
Effective length of query: 428
Effective length of database: 446
Effective search space:   190888
Effective search space used:   190888
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