GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Herbaspirillum aquaticum IEH 4430

Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate WP_039790199.1 CEJ45_RS12595 isovaleryl-CoA dehydrogenase

Query= CharProtDB::CH_091785
         (379 letters)



>NCBI__GCF_002213425.1:WP_039790199.1
          Length = 394

 Score =  293 bits (751), Expect = 4e-84
 Identities = 157/384 (40%), Positives = 241/384 (62%), Gaps = 6/384 (1%)

Query: 1   MDFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYG 60
           ++F+   +   +R+ V  FA+ E+ P AAEID +++FPM+  KK+G  G++GI   +EYG
Sbjct: 7   LNFDHGEDIAALREAVAAFAQTEIAPRAAEIDRSDQFPMDLWKKLGDLGVLGITVGEEYG 66

Query: 61  GAGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKI 120
           GAG   L++IIA+EE+S+   + G+   AH++LC + I  +G EEQK+KYL  L  G+ I
Sbjct: 67  GAGLGYLAHIIAMEEISRASASVGLSYGAHSNLCVNQIKRNGNEEQKRKYLPKLISGDFI 126

Query: 121 GAYGLTEPNAGTDSGAQQTVAVLEGDHYVINGSKIFITNGGVADTFVIFAMTDRTKGTKG 180
           GA  ++EPNAG+D  + +  A  +GD YV+NGSK++ITNG  AD  V++A TD   G +G
Sbjct: 127 GALAMSEPNAGSDVVSMKLRADKKGDRYVLNGSKMWITNGPDADVLVVYAKTDLDAGARG 186

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

Query: 241 GGRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESARYLVY 300
             R  ++   LGI +   +    Y+ +RKQFG+++ +FQ +   +ADM   + + +  VY
Sbjct: 247 FERSVLSGGPLGIMQACMDVVVPYVHDRKQFGQAIGEFQLMQGKLADMYSTMMACKAYVY 306

Query: 301 KA------AYLKQAGLPYTVDAARAKLHAANVAMDVTTKAVQLFGGYGYTKDYPVERMMR 354
                   A           DAA A L++A  A  +  +A+Q  GG GY  +YPV R+ R
Sbjct: 307 AVGQACDRADSADKVRALRKDAAGAILYSAEKATWMAGEAIQSLGGNGYINEYPVGRLWR 366

Query: 355 DAKITEIYEGTSEVQKLVISGKIF 378
           DAK+ EI  GTSE+++++I  ++F
Sbjct: 367 DAKLYEIGAGTSEIRRMLIGRELF 390


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: 403
Number of extensions: 12
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: 394
Length adjustment: 30
Effective length of query: 349
Effective length of database: 364
Effective search space:   127036
Effective search space used:   127036
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 24 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