GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Cupriavidus basilensis 4G11

Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate RR42_RS24965 RR42_RS24965 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-17424
         (375 letters)



>FitnessBrowser__Cup4G11:RR42_RS24965
          Length = 385

 Score =  299 bits (766), Expect = 8e-86
 Identities = 157/374 (41%), Positives = 236/374 (63%), Gaps = 2/374 (0%)

Query: 4   NDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDTG 63
           ND  + + D+VR F +ERL P      +    P++ + +M ++GLFGM +PE++GG +  
Sbjct: 5   NDTLEALLDSVRRFVRERLVPAEALVAETDEIPQDIVQDMRDMGLFGMTIPERFGGLELT 64

Query: 64  YVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFAL 123
                  + E+     A  +++     +G   IL  G  +Q+  +L  LATG +L +FAL
Sbjct: 65  MEEEVRVVMELCQTSPAFRSLLGTTVGIGSQGILMDGTPEQQAAWLPRLATGEILASFAL 124

Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEA-GKRGISAF 182
           TEP AGSDA SL+T A  +GDHYV+NG+K+FIT+   AG+  + A T+P+  G  G+SAF
Sbjct: 125 TEPDAGSDAGSLRTSAIKDGDHYVVNGTKRFITNAPQAGMFTLMARTNPDIKGSAGVSAF 184

Query: 183 IVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGA-EGEGYKIALANLEGGR 241
           IV   +PG    + + K+GQ  + TC ++F+NV+VP AN +G  EG+G+K A+  L+ GR
Sbjct: 185 IVDAKTPGISFGKRDVKMGQKGAHTCDVIFENVRVPAANLIGLKEGQGFKTAMKVLDKGR 244

Query: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301
           + IA+ +VG+AR     A +YA ER+ FG+P+ E Q +   LAD   ++  A  MV+ AA
Sbjct: 245 LHIAAVSVGVARRVLRDALNYALERKQFGQPISEFQLIQAMLADSQAELYAAECMVIDAA 304

Query: 302 ALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYE 361
             RD GR    EAS  K+FA+EM  +V   A+Q LGG GY+S++ +ER YRDVR+ ++YE
Sbjct: 305 RRRDEGRNVSTEASCCKMFATEMVGRVADRAVQILGGSGYISEYGIERFYRDVRLFRLYE 364

Query: 362 GTSDIQRMVIARNL 375
           GT+ IQ+++IARN+
Sbjct: 365 GTTQIQQIIIARNM 378


Lambda     K      H
   0.319    0.134    0.382 

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: 355
Number of extensions: 18
Number of successful extensions: 3
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: 375
Length of database: 385
Length adjustment: 30
Effective length of query: 345
Effective length of database: 355
Effective search space:   122475
Effective search space used:   122475
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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