GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Cola:Echvi_1686 Echvi_1686 Predicted acyl-CoA
           transferases/carnitine dehydratase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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