GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Herbaspirillum seropedicae SmR1

Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate HSERO_RS23440 HSERO_RS23440 isovaleryl-CoA dehydrogenase

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



>FitnessBrowser__HerbieS:HSERO_RS23440
          Length = 394

 Score =  256 bits (655), Expect = 6e-73
 Identities = 137/372 (36%), Positives = 227/372 (61%), Gaps = 6/372 (1%)

Query: 10  IADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDTGYVAYAM 69
           + +AV AFA   + P A + D+  +FP +   ++ +LG+ G+ V E++GG+  GY+A+ +
Sbjct: 18  LREAVAAFAHSEIAPRAAEIDRSDQFPMDLWKKLGDLGVLGITVSEEYGGAGLGYLAHII 77

Query: 70  ALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFALTEPQAG 129
           A+EEI+    +       H+++    I R GNE+QK ++L  L +G  +GA A++EP AG
Sbjct: 78  AMEEISRASASVGLSYGAHSNLCVNQIKRNGNEEQKRKYLPRLISGDFIGALAMSEPNAG 137

Query: 130 SDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAFIVPTDSP 189
           SD  S+K RA  +GD YVLNGSK +IT+G +A V++V+A TD EAG RG++AF+V     
Sbjct: 138 SDVVSMKLRADKKGDRYVLNGSKMWITNGPDADVLVVYAKTDLEAGARGMTAFLVEKGYK 197

Query: 190 GYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRIGIASQAV 249
           G+ VA+  DKLG   S T ++VF + +VP  N LG  G G  + ++ L+  R  ++   +
Sbjct: 198 GFSVAQKLDKLGMRGSHTGELVFQDCEVPEENVLGGVGRGVNVLMSGLDFERSVLSGGPL 257

Query: 250 GMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMV------LHAAAL 303
           G+ +A  +V   Y ++R+ FG+ + E Q +  +LADM + +   +  V         A  
Sbjct: 258 GIMQACMDVVVPYVHDRKQFGQAIGEFQLMQGKLADMYSTMMACKAYVYAVGQACDRADS 317

Query: 304 RDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363
            D  R    +A+ A L+++E A  +  +A+Q+LGG GY++++P+ R++RD ++ +I  GT
Sbjct: 318 ADKVRALRKDAAGAILYSAEKATWMAGEAIQSLGGNGYINEYPVGRLWRDAKLYEIGAGT 377

Query: 364 SDIQRMVIARNL 375
           S+I+RM+I R L
Sbjct: 378 SEIRRMLIGREL 389


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: 334
Number of extensions: 13
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: 375
Length of database: 394
Length adjustment: 30
Effective length of query: 345
Effective length of database: 364
Effective search space:   125580
Effective search space used:   125580
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