Align Arginase; EC 3.5.3.1 (characterized)
to candidate Dsui_0671 Dsui_0671 arginase family hydrolase, arginase/agmainase/formiminoglutamate hydrolase
Query= SwissProt::P53608 (299 letters) >FitnessBrowser__PS:Dsui_0671 Length = 292 Score = 183 bits (464), Expect = 5e-51 Identities = 110/294 (37%), Positives = 166/294 (56%), Gaps = 11/294 (3%) Query: 2 KPISIIGVPMDLGQTRRGVDMGPSAMRYAGVIERLERLHYDIEDLGDIPIGKAERLHEQG 61 + + +IG +G G GP+A+ A + L+R D+ G+ + Sbjct: 3 RTLRLIGAASGVGAQDPGCHAGPTALHRAHAFDDLQRRP-------DLSWGETLFPRQAL 55 Query: 62 DSRLRNLKAVAEANEKLAAAVDQVVQRGRFPLVLGGDHSIAIGTLAGV-AKHYERLGVIW 120 R+ VA+ ++LA AV Q +RG P+VLGGDHS AIGT +GV A +G++W Sbjct: 56 GGRVAE---VADLCQRLAEAVRQARERGETPVVLGGDHSCAIGTWSGVRAASPAPVGLLW 112 Query: 121 YDAHGDVNTAETSPSGNIHGMPLAASLGFGHPALTQIGGYSPKIKPEHVVLIGVRSLDEG 180 DAH D +T E++ SG +HGMPLA LG G L +GG PK+ P HV LIGVRS + Sbjct: 113 LDAHLDSHTPESTHSGALHGMPLACLLGQGDRRLVTVGGPGPKLLPGHVALIGVRSYEPE 172 Query: 181 EKKFIREKGIKIYTMHEVDRLGMTRVMEETIAYLKERTDGVHLSLDLDGLDPSDAPGVGT 240 E++F+ G++++T+ EV + G+ V E +A +++ G +SLDLD DP +APGVG+ Sbjct: 173 EREFLDRLGVRVFTIDEVRQRGLPAVFGEALARVRQAPGGYGVSLDLDVFDPREAPGVGS 232 Query: 241 PVIGGLTYRESHLAMEMLAEAQIITSAEFVEVNPILDERNKTASVAVALMGSLF 294 P GL+ E A+ LA + + E +E NP D +TA++ L+G++F Sbjct: 233 PEPAGLSQTELMPALAGLAGDPALLALEVMEFNPDRDAGGRTAALLARLIGAVF 286 Lambda K H 0.318 0.138 0.393 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: 248 Number of extensions: 15 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: 299 Length of database: 292 Length adjustment: 26 Effective length of query: 273 Effective length of database: 266 Effective search space: 72618 Effective search space used: 72618 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 (21.6 bits) S2: 48 (23.1 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