Align agmatinase (EC 3.5.3.11) (characterized)
to candidate GFF30 PGA1_c00300 guanidinobutyrase
Query= BRENDA::W5PHZ9 (361 letters) >FitnessBrowser__Phaeo:GFF30 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.
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:
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