GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Leeuwenhoekiella blandensis MED217

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_009779945.1 MED217_RS07745 acyl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>NCBI__GCF_000152985.1:WP_009779945.1
          Length = 602

 Score =  180 bits (457), Expect = 8e-50
 Identities = 119/391 (30%), Positives = 195/391 (49%), Gaps = 29/391 (7%)

Query: 6   EEQKLTLDMVRDVATREIAPRALELDEK--SLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63
           EEQK+  + V++   REI P     + K  +L  E  R    +LGLL   +P  Y G  M
Sbjct: 34  EEQKMMKETVKEFVDREIVPNKERFEHKDYALTEEVMRKA-GELGLLGIAVPDEYDGLGM 92

Query: 64  GVLTLALILEELGRVCASTALLLIAQTD-GMLPIIHGGSPELKERYLRRFAGESTLLTAL 122
           G ++  L+ + +     S A    A T  G +PI   G+ E K++Y+ + A       A 
Sbjct: 93  GFVSTMLVCDYISGATGSIATAFGAHTGIGTMPITLYGTEEQKKKYVPKLA-TGEWFGAY 151

Query: 123 AATEPAAGSDLLAMKTRAVRQGD--KYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGI 180
             TEP AGSD  + KT+A    D   Y INGQK +I+N    ++ +V+A  + +K    I
Sbjct: 152 CLTEPGAGSDANSGKTKAELSADGKSYKINGQKMWISNAGFCNLFIVFARIEDDKN---I 208

Query: 181 SAFVVEKGTP-GLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLS 239
           + F+VE  +  G+  G  E K+G+  S   ++FF +  VP EN++   G GF   M  L+
Sbjct: 209 TGFIVENDSSNGISLGEEEKKLGIHSSSTRQVFFNDTVVPVENMLAGRGEGFKIAMNALN 268

Query: 240 TNRVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTR 299
             R+  AA  +   +  +D+ V++  +RVQF  PIA    +++ +A+MAT        + 
Sbjct: 269 VGRIKLAAACLDAQRRIIDMGVKYANERVQFKTPIAQFGAIKYKLAEMATNAYVCESASY 328

Query: 300 KAAELLDD------------------GDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGS 341
           +AA+ ++D                  G ++  +  S+ K  AS+       + +Q+ GG 
Sbjct: 329 RAAKNIEDRIAIRMADGNSHQEAELKGVEEYAIECSILKVAASEDMQNCADEGIQIYGGM 388

Query: 342 GYMKENGVERMMRDAKLTQIYTGTNQITRMV 372
           G+  +  +E   RDA++++IY GTN+I RM+
Sbjct: 389 GFSADAPMEAAWRDARISRIYEGTNEINRML 419


Lambda     K      H
   0.319    0.134    0.371 

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: 468
Number of extensions: 26
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: 380
Length of database: 602
Length adjustment: 34
Effective length of query: 346
Effective length of database: 568
Effective search space:   196528
Effective search space used:   196528
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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