Align Arginase 1, mitochondrial; Agmatinase ARGAH1; Arginine amidohydrolase 1; EC 3.5.3.1; EC 3.5.3.11 (characterized)
to candidate PP_4523 PP_4523 putative Agmatinase
Query= SwissProt::P46637 (342 letters) >FitnessBrowser__Putida:PP_4523 Length = 320 Score = 128 bits (321), Expect = 2e-34 Identities = 90/281 (32%), Positives = 146/281 (51%), Gaps = 22/281 (7%) Query: 66 SLLGVPLGHNSSFLQGPAFAPPRIR-EAIWCGSTNSATEEGKELKDPRVLTDVGDVPVQE 124 + +GVPL +S G F P +IR E++ N AT G D + D+GDV + Sbjct: 42 AFIGVPLDIGTSLRSGTRFGPRQIRAESVMIRPYNMAT--GAAPFDSLSVADIGDVAINT 99 Query: 125 IRDCGVDDDRLMNVISESVKLVMEEEPLRPLVLGGDHSISYPVVRAVSEKLGGPVDILHL 184 + +I E+ ++E + P+ LGGDH+I+ P++RA+ +K G + ++H+ Sbjct: 100 FNLLDA-----VRIIEEAYDEIVEHNVI-PMTLGGDHTITLPILRALHKK-HGKIGLVHI 152 Query: 185 DAHPDIYDCFEGNKYSHASSFARIMEGGY--ARRLLQVGIRSINQEG------REQGKRF 236 DAH D+ D G K +H ++F R +E G R++Q+G+R+ R QG F Sbjct: 153 DAHADVNDHMFGEKIAHGTTFRRAVEEGLLDCDRVVQIGLRAQGYTADDFNWSRRQG--F 210 Query: 237 GVEQYEMRTFSKDRPMLENLKLGEGVKGVYISIDVDCLDPAFAPGVSHIEPGGLSFRDVL 296 V Q E P++ ++ G VY+S D+D +DPA+APG E GGL+ + Sbjct: 211 RVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDIDGIDPAWAPGTGTPEIGGLTTIQAM 270 Query: 297 NILHNLQA-DVVGADVVEFNPQRDTVDGMTAMVAAKLVREL 336 I+ D++G D+VE +P DT G T+++ A L+ E+ Sbjct: 271 EIIRGCHGLDLIGCDLVEVSPPYDTT-GNTSLLGANLLFEM 310 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: 303 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: 320 Length adjustment: 28 Effective length of query: 314 Effective length of database: 292 Effective search space: 91688 Effective search space used: 91688 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