GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Xanthobacter autotrophicus Py2

Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate WP_012116241.1 XAUT_RS21625 isovaleryl-CoA dehydrogenase

Query= CharProtDB::CH_091785
         (379 letters)



>NCBI__GCF_000017645.1:WP_012116241.1
          Length = 390

 Score =  306 bits (783), Expect = 8e-88
 Identities = 157/377 (41%), Positives = 236/377 (62%)

Query: 2   DFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYGG 61
           DF+L    +++R  VR F++ E+ P AAEID T +FP +   K+G  G++G+   +EYGG
Sbjct: 10  DFDLGETADMLRDTVRSFSDAEIAPRAAEIDRTNQFPRDLWPKLGALGLLGVTAEEEYGG 69

Query: 62  AGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKIG 121
           +G   L ++IA+EE+S+   + G+   AH++LC + I+ +GT EQK KYL  L  GE +G
Sbjct: 70  SGLGYLEHVIAMEEISRASASVGLSYGAHSNLCINQISRNGTAEQKAKYLPKLISGEHVG 129

Query: 122 AYGLTEPNAGTDSGAQQTVAVLEGDHYVINGSKIFITNGGVADTFVIFAMTDRTKGTKGI 181
           A  ++EP AG+D  + +T A  +GD Y++NGSK++ITNG +A+T V++A TD   G KG+
Sbjct: 130 ALAMSEPGAGSDVVSMRTRADKKGDRYILNGSKMWITNGPIAETLVVYAKTDPAAGPKGM 189

Query: 182 SAFIIEKGFKGFSIGKVEQKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTLDG 241
           +AF++E+ F GFS  +   KLG+R S T ELVF+D  VP EN++G  G+G  + M  LD 
Sbjct: 190 TAFLVERDFPGFSTAQKLDKLGMRGSDTGELVFQDCEVPEENVLGAVGRGVNVLMSGLDY 249

Query: 242 GRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESARYLVYK 301
            R  +A    GI +   +    Y+ ERKQFG+ +  FQ +   +ADM V + + +  VY 
Sbjct: 250 ERAVLAGGPTGIMQACMDIVLPYVHERKQFGQPIGTFQLMQGKIADMYVTMNATKAYVYA 309

Query: 302 AAYLKQAGLPYTVDAARAKLHAANVAMDVTTKAVQLFGGYGYTKDYPVERMMRDAKITEI 361
            A     G     DAA A L+AA  A  +  +A+Q  GG GY  DYP  R++RDAK+ EI
Sbjct: 310 VAKACDRGATTREDAAGAILYAAEKATWMALEAIQTLGGNGYINDYPTGRLLRDAKLYEI 369

Query: 362 YEGTSEVQKLVISGKIF 378
             GTSE+++++I  ++F
Sbjct: 370 GAGTSEIRRMLIGRQLF 386


Lambda     K      H
   0.317    0.135    0.377 

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: 364
Number of extensions: 10
Number of successful extensions: 1
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: 379
Length of database: 390
Length adjustment: 30
Effective length of query: 349
Effective length of database: 360
Effective search space:   125640
Effective search space used:   125640
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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