GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bcd in Pseudomonas fluorescens FW300-N2E3

Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate AO353_20350 AO353_20350 isovaleryl-CoA dehydrogenase

Query= CharProtDB::CH_091785
         (379 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_20350 AO353_20350
           isovaleryl-CoA dehydrogenase
          Length = 387

 Score =  292 bits (747), Expect = 1e-83
 Identities = 153/378 (40%), Positives = 233/378 (61%)

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

Query: 61  GAGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKI 120
           GAG   L++++A+EE+S+   +  +   AH++LC + IN +GT EQK KYL  L  GE I
Sbjct: 66  GAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGTHEQKAKYLPKLISGEHI 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 ITAFIVERDWKGFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGVLNGGVKVLMSGLD 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 AVAQACERGETTRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPAGRLLRDAKLYE 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: 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: 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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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