GapMind for catabolism of small carbon sources

 

Aligments for a candidate for speB in Phaeobacter inhibens BS107

Align agmatinase (EC 3.5.3.11) (characterized)
to candidate GFF30 PGA1_c00300 guanidinobutyrase

Query= BRENDA::W5PHZ9
         (361 letters)



>lcl|FitnessBrowser__Phaeo:GFF30 PGA1_c00300 guanidinobutyrase
          Length = 326

 Score =  155 bits (393), Expect = 1e-42
 Identities = 106/304 (34%), Positives = 158/304 (51%), Gaps = 13/304 (4%)

Query: 64  GICSMMRLPMQATPEGLDAALVGVPLDIGT-SNRPGARFGPRRIREESVMLRTANPSTGA 122
           GI ++ R P     +G D ALVGVP   G  +       GPR +R  S + R  +     
Sbjct: 17  GIPTLFRCP-NLPVDGQDIALVGVPHSAGNGTTERDQHLGPRALRNVSSVQRRMHSGFQL 75

Query: 123 VPFQFLKVADLGDVNVNLYNLQDSC-RLIRADYQKIVAAGCVPLTLGGDHTITYPILQAI 181
            P+   K+ DLGDV     N  + C + I   YQ+I  AG  P+++GGDH+IT  I+QA+
Sbjct: 76  DPWNAAKIVDLGDVPFPKANDNEDCIQQITNFYQQIDKAGARPVSVGGDHSITGGIVQAL 135

Query: 182 A----EKHGPVGLVHVDAHMDT---ADKALGEKLYHGTPFRRCVDEGLLDCKRVVQIGIR 234
                 K  P+  +H+DAH D     D  LG K           D+G +D    +QIGIR
Sbjct: 136 GCGAITKGEPICFLHLDAHTDVFTKVDHFLGAKKSAAHWGAYLADQGKVDPAHSMQIGIR 195

Query: 235 GSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDIDGLDPAYA 294
           G + TLD  + S   G+ VV  +D   + L  ++ +V + + GRP+YI+FD+D LDP  A
Sbjct: 196 GHARTLDWLQPSYEYGYNVVTMKDYRRRGLADVVAQVTEVLAGRPVYITFDLDCLDPTIA 255

Query: 295 PGTGTPEIA--GLTPSQALEIIRGCQGLNVVGCDLVEVSPPYD-PSGNTALVAANLLFEM 351
           PG    E    G     A+ ++   +G+N+VG D+V + P  D P+  TAL A  ++FE+
Sbjct: 256 PGVSNIEAGEKGFGIDDAVGLLHAVRGMNIVGGDVVCMMPTKDSPNQITALTAGAIMFEI 315

Query: 352 LCVL 355
           + ++
Sbjct: 316 ISMI 319


Lambda     K      H
   0.321    0.139    0.426 

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: 303
Number of extensions: 22
Number of successful extensions: 6
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: 361
Length of database: 326
Length adjustment: 29
Effective length of query: 332
Effective length of database: 297
Effective search space:    98604
Effective search space used:    98604
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: 49 (23.5 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