GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Pseudomonas fluorescens FW300-N1B4

Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate Pf1N1B4_3987 Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)

Query= CharProtDB::CH_091785
         (379 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3987
          Length = 387

 Score =  290 bits (741), Expect = 6e-83
 Identities = 152/378 (40%), Positives = 232/378 (61%)

Query: 1   MDFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYG 60
           ++F L    +++R  V+ F   E+ P AA+ID    FP +  +K G  G++GI   +EYG
Sbjct: 6   LNFALGETIDMLRDQVQSFVAKEIAPRAAQIDIDNLFPADLWRKFGDMGLLGITVPEEYG 65

Query: 61  GAGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKI 120
           GAG   L++++A+EE+S+   +  +   AH++LC + IN +GT EQK KYL  L  GE I
Sbjct: 66  GAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGTHEQKSKYLPKLISGEHI 125

Query: 121 GAYGLTEPNAGTDSGAQQTVAVLEGDHYVINGSKIFITNGGVADTFVIFAMTDRTKGTKG 180
           GA  ++EPNAG+D  + +  A   GDHYV+NGSK +ITNG  A+T+VI+A TD  KG  G
Sbjct: 126 GALAMSEPNAGSDVVSMKLRADKRGDHYVLNGSKTWITNGPDANTYVIYAKTDLEKGPHG 185

Query: 181 ISAFIIEKGFKGFSIGKVEQKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTLD 240
           I+AFI+E+  KGFS      KLG+R S+T EL F+D+ VP EN++G    G  + M  LD
Sbjct: 186 ITAFIVERDSKGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGVLNGGVKVLMSGLD 245

Query: 241 GGRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESARYLVY 300
             R+ ++    GI +   +    Y+ +RKQFG+S+ +FQ +   +ADM   + ++R  +Y
Sbjct: 246 YERVVLSGGPTGIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNASRAYLY 305

Query: 301 KAAYLKQAGLPYTVDAARAKLHAANVAMDVTTKAVQLFGGYGYTKDYPVERMMRDAKITE 360
             A   + G     DAA   L++A  A  +   A+Q+ GG GY  ++P  R++RDAK+ E
Sbjct: 306 AVAQACERGETARKDAAGVILYSAECATRMALDAIQILGGNGYINEFPAGRLLRDAKLYE 365

Query: 361 IYEGTSEVQKLVISGKIF 378
           I  GTSE+++++I  ++F
Sbjct: 366 IGAGTSEIRRMLIGRELF 383


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: 367
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: 387
Length adjustment: 30
Effective length of query: 349
Effective length of database: 357
Effective search space:   124593
Effective search space used:   124593
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.

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