GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocF in Dechlorosoma suillum PS

Align Arginase; EC 3.5.3.1 (characterized)
to candidate Dsui_0671 Dsui_0671 arginase family hydrolase, arginase/agmainase/formiminoglutamate hydrolase

Query= SwissProt::P53608
         (299 letters)



>FitnessBrowser__PS:Dsui_0671
          Length = 292

 Score =  183 bits (464), Expect = 5e-51
 Identities = 110/294 (37%), Positives = 166/294 (56%), Gaps = 11/294 (3%)

Query: 2   KPISIIGVPMDLGQTRRGVDMGPSAMRYAGVIERLERLHYDIEDLGDIPIGKAERLHEQG 61
           + + +IG    +G    G   GP+A+  A   + L+R         D+  G+     +  
Sbjct: 3   RTLRLIGAASGVGAQDPGCHAGPTALHRAHAFDDLQRRP-------DLSWGETLFPRQAL 55

Query: 62  DSRLRNLKAVAEANEKLAAAVDQVVQRGRFPLVLGGDHSIAIGTLAGV-AKHYERLGVIW 120
             R+     VA+  ++LA AV Q  +RG  P+VLGGDHS AIGT +GV A     +G++W
Sbjct: 56  GGRVAE---VADLCQRLAEAVRQARERGETPVVLGGDHSCAIGTWSGVRAASPAPVGLLW 112

Query: 121 YDAHGDVNTAETSPSGNIHGMPLAASLGFGHPALTQIGGYSPKIKPEHVVLIGVRSLDEG 180
            DAH D +T E++ SG +HGMPLA  LG G   L  +GG  PK+ P HV LIGVRS +  
Sbjct: 113 LDAHLDSHTPESTHSGALHGMPLACLLGQGDRRLVTVGGPGPKLLPGHVALIGVRSYEPE 172

Query: 181 EKKFIREKGIKIYTMHEVDRLGMTRVMEETIAYLKERTDGVHLSLDLDGLDPSDAPGVGT 240
           E++F+   G++++T+ EV + G+  V  E +A +++   G  +SLDLD  DP +APGVG+
Sbjct: 173 EREFLDRLGVRVFTIDEVRQRGLPAVFGEALARVRQAPGGYGVSLDLDVFDPREAPGVGS 232

Query: 241 PVIGGLTYRESHLAMEMLAEAQIITSAEFVEVNPILDERNKTASVAVALMGSLF 294
           P   GL+  E   A+  LA    + + E +E NP  D   +TA++   L+G++F
Sbjct: 233 PEPAGLSQTELMPALAGLAGDPALLALEVMEFNPDRDAGGRTAALLARLIGAVF 286


Lambda     K      H
   0.318    0.138    0.393 

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: 248
Number of extensions: 15
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: 299
Length of database: 292
Length adjustment: 26
Effective length of query: 273
Effective length of database: 266
Effective search space:    72618
Effective search space used:    72618
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 (21.6 bits)
S2: 48 (23.1 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