GapMind for catabolism of small carbon sources

 

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

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Echvi_1686 Echvi_1686 Predicted acyl-CoA transferases/carnitine dehydratase

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>FitnessBrowser__Cola:Echvi_1686
          Length = 387

 Score =  168 bits (425), Expect = 3e-46
 Identities = 118/382 (30%), Positives = 188/382 (49%), Gaps = 19/382 (4%)

Query: 9   VLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEAAYYLS 68
           VL+  + L+GP AG  LADLGA VIK+E PG GD  R      +K+   EN  ++  + +
Sbjct: 19  VLEFCQYLSGPSAGLRLADLGARVIKIENPGKGDLCRILP---IKNRWVEN--DSLLFHT 73

Query: 69  ANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINPQLIYC 128
            NRNK+S T +         ++ L  K+D+L+ NF+ G +   GL Y+++KA+N  L+Y 
Sbjct: 74  INRNKESYTANLKSEHELAEIKRLIGKADVLMHNFRPGVMEKLGLGYEAVKALNAGLVYA 133

Query: 129 SITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTGLYSTA 188
            I+G+G  GP+A++ G D ++Q + GLM  +    G++  GP+  G+A+ D+L G  +  
Sbjct: 134 EISGYGAEGPWARKPGQDLLLQAMSGLMFAS----GNQKDGPMPFGLAIGDMLCGAQAVQ 189

Query: 189 AILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKR--LGNAHPNI-VPY 245
            ILAAL HR   G G  I ++LL+  +         Y  +G  P R  + +AHP +  PY
Sbjct: 190 GILAALVHRKRTGKGSRISLSLLESLLDMQFEVLTTYFASGKRPLRSAVNSAHPLLGAPY 249

Query: 246 QDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQATV 305
             + T D    + +      R+ A   G+ +  D     T+  R A + VL   ++ A  
Sbjct: 250 GIYATKDSHLAIAMIPIAPLRE-ALGCGELERFDQSMVFTH--RDAIKQVLADFLKSA-- 304

Query: 306 FKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPIRLS 365
             TT  W+ +L + G+    + D  Q+ A    +   L   +       +     PIR+ 
Sbjct: 305 --TTDHWLAKLREKGLWAMDVKDWKQLKATQGYRQSNLEQIIKLTNGQSIKTNRCPIRID 362

Query: 366 ETPVEYRNAPPLLGEHTLEVLQ 387
              +      P LGEHT  + Q
Sbjct: 363 GEVLLSDRPAPTLGEHTASIKQ 384


Lambda     K      H
   0.319    0.137    0.408 

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: 396
Number of extensions: 18
Number of successful extensions: 4
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: 406
Length of database: 387
Length adjustment: 31
Effective length of query: 375
Effective length of database: 356
Effective search space:   133500
Effective search space used:   133500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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