Align guanidinobutyrase subunit (EC 3.5.3.7) (characterized)
to candidate Pf1N1B4_525 Agmatinase (EC 3.5.3.11)
Query= metacyc::MONOMER-11557 (320 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_525 Length = 316 Score = 610 bits (1573), Expect = e-179 Identities = 295/316 (93%), Positives = 306/316 (96%) Query: 5 VDKTLHQPLGGNEMPRFGGIATMLRLPHLQSAKGLDAAFIGVPLDIGTSLRSGTRFGPRQ 64 VDK LHQPLGGNEMPRFGGIATMLRLPHL SA GLDAAFIG+PLDIGTSLR GTRFGPR+ Sbjct: 1 VDKILHQPLGGNEMPRFGGIATMLRLPHLPSAAGLDAAFIGIPLDIGTSLRPGTRFGPRE 60 Query: 65 IRAESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEIVEHNVIPM 124 IRAESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYD I+EH+VIP+ Sbjct: 61 IRAESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDNILEHDVIPL 120 Query: 125 TLGGDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGLLDC 184 TLGGDHTITLPILRA+HKKHGK+GLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGLLDC Sbjct: 121 TLGGDHTITLPILRAIHKKHGKVGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGLLDC 180 Query: 185 DRVVQIGLRAQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFD 244 DRVVQIGLRAQGYTADDFNWSR QGFRVVQAEECWHKSL PLMAEVREKVGGGPVYLSFD Sbjct: 181 DRVVQIGLRAQGYTADDFNWSRNQGFRVVQAEECWHKSLAPLMAEVREKVGGGPVYLSFD 240 Query: 245 IDGIDPAWAPGTGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTSLLGA 304 IDGIDPAWAPGTGTPEIGGLTTIQA+EI+RGC GLDL+GCDLVEVSP YDTTGNTSLLGA Sbjct: 241 IDGIDPAWAPGTGTPEIGGLTTIQAIEIVRGCQGLDLVGCDLVEVSPAYDTTGNTSLLGA 300 Query: 305 NLLFEMLCVLPGVVRR 320 NLL+EMLCVLPGVV R Sbjct: 301 NLLYEMLCVLPGVVHR 316 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: 557 Number of extensions: 16 Number of successful extensions: 2 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: 316 Length adjustment: 27 Effective length of query: 293 Effective length of database: 289 Effective search space: 84677 Effective search space used: 84677 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