Align guanidinobutyrase subunit (EC 3.5.3.7) (characterized)
to candidate BPHYT_RS31515 BPHYT_RS31515 agmatinase
Query= metacyc::MONOMER-11557 (320 letters) >FitnessBrowser__BFirm:BPHYT_RS31515 Length = 324 Score = 310 bits (794), Expect = 3e-89 Identities = 150/308 (48%), Positives = 210/308 (68%), Gaps = 6/308 (1%) Query: 12 PLGGNEMPRFGGIATMLRLPHLQ----SAKGLDAAFIGVPLDIGTSLRSGTRFGPRQIRA 67 P+ G MPR+ G+AT++RLPH++ S K +D IGVP D GT+ R G R GPRQ+R Sbjct: 8 PVTGTMMPRYAGVATLMRLPHMELTNNSIKDVDIGLIGVPWDGGTTNRPGARHGPRQVRD 67 Query: 68 ESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEIVEHNVIPMTLG 127 S M+R N ++ PF + AD+GD +N +L+D++ I YDE+ + + P+++G Sbjct: 68 ISTMVRNVNRSSNINPFGLCNCADLGDAPVNPVDLIDSLNRIAGFYDEVCKLGIAPLSVG 127 Query: 128 GDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKI-AHGTTFRRAVEEGLLDCDR 186 GDH +TLPI+R L K +G+VH DAH D + FG+ I HGT FRRA+EEGLLD R Sbjct: 128 GDHLVTLPIMRGLAKDR-PLGMVHFDAHTDTWNRYFGDNIYTHGTPFRRAIEEGLLDPKR 186 Query: 187 VVQIGLRAQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDID 246 VQIG+R Y + +W R+G RV+ +E ++ ++ E R VG GP Y++FD+D Sbjct: 187 TVQIGIRGALYNDSENDWGEREGIRVIDIDEFHAMGIDAVIQEARRVVGDGPTYVTFDVD 246 Query: 247 GIDPAWAPGTGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTSLLGANL 306 +DP +APGTGTPEIGGLTT++A +IRG GL+L+G D+VEVSPP+D +GNT+L+GA L Sbjct: 247 ALDPVFAPGTGTPEIGGLTTLEAQHMIRGLRGLNLVGGDVVEVSPPFDPSGNTALVGATL 306 Query: 307 LFEMLCVL 314 +FE+LCVL Sbjct: 307 MFEILCVL 314 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: 401 Number of extensions: 21 Number of successful extensions: 4 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: 324 Length adjustment: 28 Effective length of query: 292 Effective length of database: 296 Effective search space: 86432 Effective search space used: 86432 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