Align Arginase 1, mitochondrial; Agmatinase ARGAH1; Arginine amidohydrolase 1; EC 3.5.3.1; EC 3.5.3.11 (characterized)
to candidate BPHYT_RS05090 BPHYT_RS05090 agmatinase
Query= SwissProt::P46637 (342 letters) >FitnessBrowser__BFirm:BPHYT_RS05090 Length = 329 Score = 117 bits (293), Expect = 4e-31 Identities = 90/285 (31%), Positives = 138/285 (48%), Gaps = 34/285 (11%) Query: 68 LGVPLGHNSSFLQGPAFAPPRIR-EAIWCGSTNSATEEGKELKDPRVLTDVGDVPVQEIR 126 +GVP +S G F P +IR E++ N AT D + D+GDV + Sbjct: 49 VGVPFDLGTSNRTGARFGPRQIRSESVLLRPYNMATRAAPF--DSLRVADLGDVAINPYN 106 Query: 127 DCGVDDDRLMNVISESVKLV------MEEEPLRPLVLGGDHSISYPVVRAVSEKLGGPVD 180 + +S+K + + + +P+ LGGDH+I+ P++RA+ K G V Sbjct: 107 ------------LHDSIKRIETAYDEILQHDCKPITLGGDHTIALPILRAIHRK-HGKVG 153 Query: 181 ILHLDAHPDIYDCFEGNKYSHASSFARIMEGGY--ARRLLQVGIRSINQEG------REQ 232 ++H+DAH D+ D G K +H + F R +E G R++Q+G+R R+Q Sbjct: 154 LIHVDAHADVNDTMMGEKIAHGTPFRRAVEEGLLDCDRVVQIGLRGTGYAAEDFDWCRDQ 213 Query: 233 GKRFGVEQYEMRTFSKDRPMLENLKLGEGVKGVYISIDVDCLDPAFAPGVSHIEPGGLSF 292 G F V Q E P++ ++ G VYI+ D+D +DPAFAPG E GL+ Sbjct: 214 G--FEVVQAEACWNQSLVPLMARIRERMGDGPVYITFDIDGIDPAFAPGTGTPEIAGLTV 271 Query: 293 RDVLNILHNLQA-DVVGADVVEFNPQRDTVDGMTAMVAAKLVREL 336 L I+ + ++VG D+VE P D G TA++ A L EL Sbjct: 272 PQALEIIRGSRGLNIVGCDLVEVAPPYDPF-GTTALLGANLAFEL 315 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: 281 Number of extensions: 14 Number of successful extensions: 3 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: 329 Length adjustment: 28 Effective length of query: 314 Effective length of database: 301 Effective search space: 94514 Effective search space used: 94514 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