GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Echinicola vietnamensis KMM 6221, DSM 17526

Align Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::Q8GAK7
         (458 letters)



>FitnessBrowser__Cola:Echvi_3822
          Length = 453

 Score =  394 bits (1013), Expect = e-114
 Identities = 207/452 (45%), Positives = 286/452 (63%), Gaps = 3/452 (0%)

Query: 5   TIDPTTGITLKTFDAHTPEEVENRIARAEAAFRSLQNTSFEERARWMHKAADILESEADE 64
           +I+P TG  L+ F  HT ++VE  I + + A+ S +     +RA  M KA  +L    D+
Sbjct: 3   SINPYTGELLEEFTDHTEQQVEAAIQKGQEAYLSWRELPISQRADLMKKAGQVLRDNTDK 62

Query: 65  VARLIATEMGKTLTTAKYEALKSATGMRHFADHAQRYLSPETPVPASEVNASNLHVQFDP 124
             ++I+ EMGK +T +K E  K A    ++A++A+  L+     P +  +     V ++P
Sbjct: 63  YGKIISLEMGKVITESKSEVEKCAWVCEYYAENAEEMLAD---APIALPDGKEAKVVYNP 119

Query: 125 LGVVLAVMPWNYPLWQAVRFAAPALMAGNTGLLKHASNVPQCALYLGDLFARGGFPEGAF 184
           LG+VLAVMPWN+P WQ  RFAAP L AGN GLLKHASNVPQCAL + ++F + GFPEG F
Sbjct: 120 LGIVLAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPEGVF 179

Query: 185 QTLLVEGKDVIPLVDDARIRAVTLTGSVAAGSAIAEAAGRNIKRSVLELGGMDVFIVMPS 244
           Q+LL+    V  ++    ++A TLTGS  AG  IA  AG  IK++VLELGG D FIV+  
Sbjct: 180 QSLLIGSDKVANIIAHPDVKAATLTGSEKAGQKIAAQAGEQIKKTVLELGGSDPFIVLKD 239

Query: 245 ADIEKAAAQAVIARLQNSGQSCIAAKRFYVHEDVYDRFEHLFVTGMAEAVAGDPLDESTS 304
           AD+++AA  A   R+ N GQSCIAAKRF + ++VYD F   F + +   V GDPLDE   
Sbjct: 240 ADVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPLDEKAG 299

Query: 305 FGPLATERGRQDVHELVRDAREKGAAVQCGGEIPEGEGWYYPATVLTGVTEDMRIYREEC 364
           +  +A      +++E V  + +KGA V   G  PE    +    +L  +T DM  YREE 
Sbjct: 300 YACMARPDLAMELYEQVEASIQKGAEVILEGTKPEKGKAFIKPYILGKLTPDMPAYREEL 359

Query: 365 FGPVACLYKVSSLQEAIALSNDSDFGLSSSVWTNDETEATEAARSIEAGGVFINGLTASF 424
           FGPVA ++K + + EAIA++NDS FGL +S+WT D  +A   +R IE+G VFIN + AS 
Sbjct: 360 FGPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFINSMVASN 419

Query: 425 PAVPFGGLKDSGYGRELSAYGIREFVNIKTVW 456
           P +PFGG+K SGYGREL+  GI+EF+NIKTV+
Sbjct: 420 PYLPFGGIKKSGYGRELAENGIKEFMNIKTVY 451


Lambda     K      H
   0.317    0.132    0.386 

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: 463
Number of extensions: 19
Number of successful extensions: 2
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: 458
Length of database: 453
Length adjustment: 33
Effective length of query: 425
Effective length of database: 420
Effective search space:   178500
Effective search space used:   178500
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 (21.7 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