GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acdH in Dechlorosoma suillum PS

Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate Dsui_0975 Dsui_0975 acyl-CoA dehydrogenase

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



>lcl|FitnessBrowser__PS:Dsui_0975 Dsui_0975 acyl-CoA dehydrogenase
          Length = 390

 Score =  254 bits (649), Expect = 3e-72
 Identities = 139/371 (37%), Positives = 215/371 (57%), Gaps = 3/371 (0%)

Query: 8   QQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDTGYVAY 67
           + + D VRAFA + + P A Q D+D+ FP +   +  +LGL GM   E++GG+  GY+A+
Sbjct: 15  EMLRDTVRAFAAKEIAPRAAQIDRDNEFPADLWQKFGDLGLLGMTAEEEYGGTAMGYLAH 74

Query: 68  AMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFALTEPQ 127
            +A+EEI+    +       H+++    I R G   QK ++L  L +G  +GA A++EP 
Sbjct: 75  IVAMEEISRASASVGLSYGAHSNLCVNQIRRNGTAAQKAKYLPGLISGTQVGALAMSEPN 134

Query: 128 AGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAFIVPTD 187
           AGSD  S+K +A  +GD YVLNGSK +IT+G +A  ++V+A TD  AG +G++AFIV   
Sbjct: 135 AGSDVVSMKLKAEKKGDRYVLNGSKMWITNGGDADTLVVYAKTDLNAGAKGMTAFIVEKG 194

Query: 188 SPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRIGIASQ 247
             G+      DKLG   S+T  + FD+ +VP  N LG  G G K+ ++ L+  R  +   
Sbjct: 195 FKGFSHGTHLDKLGMRGSNTFPLFFDDCEVPEENVLGGVGNGAKVLMSGLDYERAVLCGG 254

Query: 248 AVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVL---HAAALR 304
            +G+  A  +V   Y +ER+ FG  + E Q +  +LADM +     R  V     A    
Sbjct: 255 PLGIMAACMDVVLPYLHEREQFGTAIGEFQLMQGKLADMYSTWQATRAYVYAVGQACDRA 314

Query: 305 DAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTS 364
           D  R    +A+ A L+++E A  +  DA+QTLGG GY +++P  R++RD ++ +I  GTS
Sbjct: 315 DHARSLRKDAAGAILYSAEKATWMAGDAIQTLGGVGYTNEYPTGRLWRDAKLYEIGAGTS 374

Query: 365 DIQRMVIARNL 375
           +I+RM+I R L
Sbjct: 375 EIRRMLIGREL 385


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: 326
Number of extensions: 13
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: 390
Length adjustment: 30
Effective length of query: 345
Effective length of database: 360
Effective search space:   124200
Effective search space used:   124200
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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