GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Burkholderia phytofirmans PsJN

Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate BPHYT_RS23260 BPHYT_RS23260 isovaleryl-CoA dehydrogenase

Query= CharProtDB::CH_091785
         (379 letters)



>FitnessBrowser__BFirm:BPHYT_RS23260
          Length = 393

 Score =  296 bits (757), Expect = 9e-85
 Identities = 157/383 (40%), Positives = 238/383 (62%), Gaps = 5/383 (1%)

Query: 1   MDFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYG 60
           + F L  E E++R  +  FA  E+ P AAEID T++FPM+  +K G  G++G+  S+EYG
Sbjct: 7   LQFPLGEEIEMLRDSIAGFAAKEIAPRAAEIDRTDQFPMDLWRKFGDLGVLGMTVSEEYG 66

Query: 61  GAGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKI 120
           GA     +++IA+EE+S+   + G+   AH++LC + I+ +GTE QKQKYL  L  GE +
Sbjct: 67  GANMGYTAHMIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEAQKQKYLPKLVSGEHV 126

Query: 121 GAYGLTEPNAGTDSGAQQTVAVLEGDHYVINGSKIFITNGGVADTFVIFAMTDRTKGTKG 180
           GA  ++EPNAG+D  + +  A  +GDHYV+NG+K++ITNG   DT V++A TD    ++G
Sbjct: 127 GALAMSEPNAGSDVVSMKLRAEKKGDHYVLNGTKMWITNGPDCDTLVVYAKTDPEANSRG 186

Query: 181 ISAFIIEKGFKGFSIGKVEQKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTLD 240
           I+AFI+EKG KGFS+ +   KLG+R S T ELVF+D+ VP EN++G+   G  + M  LD
Sbjct: 187 ITAFIVEKGMKGFSVAQKLDKLGMRGSHTGELVFQDVEVPEENILGQLNGGAKVLMSGLD 246

Query: 241 GGRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESAR-YLV 299
             R  +A    GI     +    Y+ +RKQFG+S+ +FQ +   +AD+   +++ R YL 
Sbjct: 247 YERAVLAGGPTGIMVAVMDAVVPYIHDRKQFGQSIGEFQLIQGKVADLYTTLQACRAYLY 306

Query: 300 YKAAYLKQAGLPYT----VDAARAKLHAANVAMDVTTKAVQLFGGYGYTKDYPVERMMRD 355
                L   G  +      D A   L+ A  A  +  +A+Q+ GG GY  +YPV R+ RD
Sbjct: 307 AVGRQLDTLGKEHVRQVRKDCAGVILYTAEKATWMAGEAIQILGGNGYINEYPVGRLWRD 366

Query: 356 AKITEIYEGTSEVQKLVISGKIF 378
           AK+ EI  GTSE+++++I  ++F
Sbjct: 367 AKLYEIGAGTSEIRRMLIGRELF 389


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: 396
Number of extensions: 10
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: 379
Length of database: 393
Length adjustment: 30
Effective length of query: 349
Effective length of database: 363
Effective search space:   126687
Effective search space used:   126687
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 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