Align guanidinobutyrase subunit (EC 3.5.3.7) (characterized)
to candidate PfGW456L13_2989 Agmatinase (EC 3.5.3.11)
Query= metacyc::MONOMER-11557 (320 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2989 Length = 319 Score = 235 bits (600), Expect = 9e-67 Identities = 131/298 (43%), Positives = 176/298 (59%), Gaps = 17/298 (5%) Query: 21 FGGIATMLRLPHLQSAKGLDAAFIGVPLDIGTSLRSGTRFGPRQIRAESVMIR-----PY 75 + GI + +R + + +G+D A GVP D TS R G RFGPR IRA S I P+ Sbjct: 25 YAGITSFMRRRYSRDLRGVDVAVSGVPFDTATSNRPGARFGPRGIRAASAGIAWERHWPW 84 Query: 76 NMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEIVEHNVIPMTLGGDHTITLP 135 PFD L+V D GD + + +IE + I+ +T GGDH IT P Sbjct: 85 TFD----PFDHLAVIDYGDCDFDYGSPQSTPEMIEAHAEHILNAGTAMLTFGGDHFITYP 140 Query: 136 ILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGLLDCDRVVQIGLRAQ 195 +L+A +KHG + L+H DAH+D G++I HGT F A EGL+D R VQIGLR Sbjct: 141 LLKAHARKHGALSLIHFDAHSDTWPDEEGKRIDHGTMFWHAAREGLVDPSRSVQIGLRT- 199 Query: 196 GYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDIDGIDPAWAPG 255 T DD QGF V+ A + + E ++ +R +VG PVYL+FDID +DPA+APG Sbjct: 200 --TNDD-----HQGFEVLDARQVHRRGCEAIVEAIRARVGDNPVYLTFDIDCLDPAFAPG 252 Query: 256 TGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTSLLGANLLFEMLCV 313 TGTP GGL+T+QA+EI+ G G++L+G D+VEV+P YD+ TSL A L EMLC+ Sbjct: 253 TGTPVCGGLSTVQALEILGGLRGINLVGMDVVEVAPAYDSAEITSLAAATLAMEMLCL 310 Lambda K H 0.322 0.141 0.431 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: 357 Number of extensions: 19 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: 320 Length of database: 319 Length adjustment: 28 Effective length of query: 292 Effective length of database: 291 Effective search space: 84972 Effective search space used: 84972 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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