Align Arginase 1, mitochondrial; Arginine amidohydrolase 1; EC 3.5.3.1 (characterized)
to candidate BPHYT_RS31515 BPHYT_RS31515 agmatinase
Query= SwissProt::B8AU84 (340 letters) >FitnessBrowser__BFirm:BPHYT_RS31515 Length = 324 Score = 107 bits (266), Expect = 5e-28 Identities = 88/289 (30%), Positives = 146/289 (50%), Gaps = 28/289 (9%) Query: 65 LLGVPLGHNSSFLQGPAFAPPRIREAIWCGSTNSSTEEGKELNDPRVL---TDVGDVPIQ 121 L+GVP ++ G P ++R+ ST +P L D+GD P+ Sbjct: 43 LIGVPWDGGTTNRPGARHGPRQVRDI----STMVRNVNRSSNINPFGLCNCADLGDAPVN 98 Query: 122 EIRDCGVEDDRLMNVVSESVKTVMEEDPLRPLVLGGDHSISYPVVRAVSEKLGGPVDILH 181 + D +R+ E K + PL +GGDH ++ P++R +++ P+ ++H Sbjct: 99 PV-DLIDSLNRIAGFYDEVCKL-----GIAPLSVGGDHLVTLPIMRGLAKDR--PLGMVH 150 Query: 182 LDAHPDIYDAFEG-NIYSHASSFARIMEGGYA--RRLLQVGIRSITKEGREQ--GKRFGV 236 DAH D ++ + G NIY+H + F R +E G +R +Q+GIR E G+R G+ Sbjct: 151 FDAHTDTWNRYFGDNIYTHGTPFRRAIEEGLLDPKRTVQIGIRGALYNDSENDWGEREGI 210 Query: 237 EQYEMRTFSK---DREKLESLKL-GEGVKGVYISVDVDCLDPAFAPGVSHIEPGGLSFRD 292 ++ F D E+ ++ G+G Y++ DVD LDP FAPG E GGL+ + Sbjct: 211 RVIDIDEFHAMGIDAVIQEARRVVGDGP--TYVTFDVDALDPVFAPGTGTPEIGGLTTLE 268 Query: 293 VLNILHNLQG-DVVAGDVVEFNPQRDTVDGMTAMVAAKLVRELTAKISK 340 +++ L+G ++V GDVVE +P D G TA+V A L+ E+ +++ Sbjct: 269 AQHMIRGLRGLNLVGGDVVEVSPPFDP-SGNTALVGATLMFEILCVLAE 316 Lambda K H 0.318 0.137 0.394 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: 289 Number of extensions: 10 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: 340 Length of database: 324 Length adjustment: 28 Effective length of query: 312 Effective length of database: 296 Effective search space: 92352 Effective search space used: 92352 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