Align Arginase 1, mitochondrial; Agmatinase ARGAH1; Arginine amidohydrolase 1; EC 3.5.3.1; EC 3.5.3.11 (characterized)
to candidate RR42_RS02455 RR42_RS02455 agmatinase
Query= SwissProt::P46637 (342 letters) >FitnessBrowser__Cup4G11:RR42_RS02455 Length = 328 Score = 115 bits (287), Expect = 2e-30 Identities = 93/291 (31%), Positives = 142/291 (48%), Gaps = 27/291 (9%) Query: 61 AKASTS-----LLGVPLGHNSSFLQGPAFAPPRIR-EAIWCGSTNSATEEGKELKDPRVL 114 A AST+ +GVP +S G P +IR E++ N AT D + Sbjct: 38 AAASTAGLDACFVGVPFDLGTSNRNGARLGPRQIRAESVLLRPYNMATRAAPF--DSLRV 95 Query: 115 TDVGDVPVQEIRDCGVDDDRLMNVISESVKLVMEEEPLRPLVLGGDHSISYPVVRAVSEK 174 D+GDV D + + E+ + RP+ LGGDH+++ P++RA+ + Sbjct: 96 ADIGDVATNPYNL----HDAIARI--EAAYRDIIATGCRPIGLGGDHTVTLPILRAMHAR 149 Query: 175 LGGPVDILHLDAHPDIYDCFEGNKYSHASSFARIMEGGY--ARRLLQVGIRSINQEG--- 229 G + ++H+DAH D+ D G K +H + F R +E G R++Q+G+R Sbjct: 150 -HGRLGLIHVDAHADVNDTMFGEKIAHGTPFRRAVEEGLLDCGRVVQIGLRGTGYAAEDF 208 Query: 230 ---REQGKRFGVEQYEMRTFSKDRPMLENLKLGEGVKGVYISIDVDCLDPAFAPGVSHIE 286 R+QG F V E + P++E + + VYIS D+D +DPA+APG E Sbjct: 209 DWCRQQG--FRVITAEACWYRSLAPLMEEIGMRLQGGPVYISFDIDGIDPAYAPGTGTPE 266 Query: 287 PGGLSFRDVLNILHNLQA-DVVGADVVEFNPQRDTVDGMTAMVAAKLVREL 336 GGL+ L I+ + D+VGAD+VE +P D G TA++ A L EL Sbjct: 267 IGGLTVPQALEIIRGARGLDIVGADLVEVSPPYDPF-GTTALLGANLAFEL 316 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: 287 Number of extensions: 16 Number of successful extensions: 4 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: 342 Length of database: 328 Length adjustment: 28 Effective length of query: 314 Effective length of database: 300 Effective search space: 94200 Effective search space used: 94200 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