GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PS:Dsui_0975
          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 (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