Align Arginase 1, mitochondrial; Agmatinase ARGAH1; Arginine amidohydrolase 1; EC 3.5.3.1; EC 3.5.3.11 (characterized)
to candidate GFF3941 PS417_20180 agmatinase
Query= SwissProt::P46637 (342 letters) >FitnessBrowser__WCS417:GFF3941 Length = 316 Score = 130 bits (326), Expect = 6e-35 Identities = 95/283 (33%), Positives = 150/283 (53%), Gaps = 26/283 (9%) Query: 66 SLLGVPLGHNSSFLQGPAFAPPRIR-EAIWCGSTNSATEEGKELKDPRVLTDVGDVPVQE 124 + +GVPL +S G F P IR E++ N AT G D + D+GDV + Sbjct: 38 AFIGVPLDIGTSLRAGTRFGPREIRAESVMIRPYNMAT--GAAPFDSLSVADIGDVAINT 95 Query: 125 IRDCGVDDDRLMNVISESVKLVMEEEPLRPLVLGGDHSISYPVVRAVSEKLGGPVDILHL 184 + +I E+ ++E + + PL LGGDH+I+ P++RA+ +K G V ++H+ Sbjct: 96 FNLLDA-----VRIIEEAYDEILEHDVI-PLTLGGDHTITLPILRAIHKK-HGKVGLVHI 148 Query: 185 DAHPDIYDCFEGNKYSHASSFARIMEGGY--ARRLLQVGIRSINQEG------REQGKRF 236 DAH D+ D G K +H ++F R +E G R++Q+G+R+ R+QG F Sbjct: 149 DAHADVNDHMFGEKIAHGTTFRRAVEEGLLDCDRVVQIGLRAQGYTAEDFNWSRKQG--F 206 Query: 237 GVEQYEMRTFSKDRPMLENLKLGEGVKG--VYISIDVDCLDPAFAPGVSHIEPGGLSFRD 294 V Q E P++ ++ E V G VY+S D+D +DPA+APG E GGL+ Sbjct: 207 RVVQAEECWHHSLAPLMAEVR--EKVDGGPVYLSFDIDGIDPAWAPGTGTPEIGGLTTIQ 264 Query: 295 VLNILHNLQA-DVVGADVVEFNPQRDTVDGMTAMVAAKLVREL 336 + I+ Q D++G D+VE +P DT G T+++ A L+ E+ Sbjct: 265 AIEIIRGCQGLDLIGCDLVEVSPPYDTT-GNTSLLGANLLYEM 306 Lambda K H 0.318 0.137 0.392 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: 279 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 342 Length of database: 316 Length adjustment: 28 Effective length of query: 314 Effective length of database: 288 Effective search space: 90432 Effective search space used: 90432 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 (21.7 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