Align guanidinobutyrase subunit (EC 3.5.3.7) (characterized)
to candidate BWI76_RS21880 BWI76_RS21880 agmatinase
Query= metacyc::MONOMER-11557 (320 letters) >FitnessBrowser__Koxy:BWI76_RS21880 Length = 316 Score = 504 bits (1297), Expect = e-147 Identities = 240/313 (76%), Positives = 271/313 (86%) Query: 5 VDKTLHQPLGGNEMPRFGGIATMLRLPHLQSAKGLDAAFIGVPLDIGTSLRSGTRFGPRQ 64 +D HQP GGNEMPRFGG ATM+RLP + + +GLDAAF+G+PLDIGTS RSGTR+GPR Sbjct: 1 MDNVFHQPQGGNEMPRFGGRATMMRLPFIDNLQGLDAAFVGIPLDIGTSQRSGTRYGPRY 60 Query: 65 IRAESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEIVEHNVIPM 124 IR ESVMIRPYNMATGAAPFDSLSVADIGDV INT+NLL +V+IIE+ Y + +IP+ Sbjct: 61 IRTESVMIRPYNMATGAAPFDSLSVADIGDVPINTYNLLKSVQIIEDYYTGLNSFPLIPL 120 Query: 125 TLGGDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGLLDC 184 TLGGDHTITLPILRAL KKHG +GL+HIDAH D ND MFGEKIAHGTTFRRAVEEGLLD Sbjct: 121 TLGGDHTITLPILRALTKKHGPVGLIHIDAHTDTNDEMFGEKIAHGTTFRRAVEEGLLDL 180 Query: 185 DRVVQIGLRAQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFD 244 RVVQIG RAQGY A DF W +GFR+VQAE+CWHKSL PLMAEVR+++G GPVYLSFD Sbjct: 181 KRVVQIGQRAQGYAAGDFQWGVDRGFRLVQAEQCWHKSLAPLMAEVRQQMGDGPVYLSFD 240 Query: 245 IDGIDPAWAPGTGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTSLLGA 304 ID +DP WAPGTGTPE+GGLT+IQA+EI+RGC GL+LIGCDLVEVSPPYD +GNTS L A Sbjct: 241 IDSLDPIWAPGTGTPEVGGLTSIQALEIVRGCRGLNLIGCDLVEVSPPYDVSGNTSQLAA 300 Query: 305 NLLFEMLCVLPGV 317 NLL+EMLCVLPGV Sbjct: 301 NLLYEMLCVLPGV 313 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: 451 Number of extensions: 18 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