Align Guanidinobutyrase; EC 3.5.3.7 (characterized)
to candidate GFF31 PGA1_c00310 guanidinobutyrase
Query= SwissProt::Q9I3S3 (319 letters) >FitnessBrowser__Phaeo:GFF31 Length = 324 Score = 305 bits (781), Expect = 1e-87 Identities = 152/314 (48%), Positives = 205/314 (65%), Gaps = 3/314 (0%) Query: 8 PLGGNEMPRFGGIATMMRLPHVQ-SPAELDALDAAFVGVPLDIGTSLRSGTRFGPREIRA 66 P+ G EMPRF G+ T MRLPHV S +D + VGVP D GT+ R G R GPR++R Sbjct: 11 PVSGMEMPRFAGLPTFMRLPHVTVSDPIIDQVQLGLVGVPWDAGTTNRPGPRHGPRQLRD 70 Query: 67 ESVMIRPYNMATGAAPFDSLNVADIGDVAINTFNLLEAVRIIEQEYDRILGHGILPLTLG 126 S MIR N TG PF +N AD+GDVA N ++++ + I Y + I LT+G Sbjct: 71 LSTMIRAGNPVTGINPFSMINCADLGDVAPNPVDIIDCMERISAFYADLKSRDIFALTVG 130 Query: 127 GDHTITLPILRAIKKKHGKVGLVHVDAHADVNDHMFG-EKIAHGTTFRRAVEEDLLDCDR 185 GDH ++LP+LR + VGL+ D+H D+ D FG K HGT FRRA+EE L+D R Sbjct: 131 GDHLVSLPVLRGLASG-APVGLIQFDSHTDLFDSYFGGNKYTHGTPFRRAIEEGLVDPKR 189 Query: 186 VVQIGLRAQGYTAEDFNWSRKQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDID 245 +VQIG+R Y ED W + QG R+++ EE + + + +M EVRE VG P Y ++DID Sbjct: 190 MVQIGIRGTAYNTEDVEWGQAQGVRIIRIEEFFDRGVSDVMREVREIVGDQPTYCTYDID 249 Query: 246 GIDPAWAPGTGTPEIGGLTTIQAMEIIRGCQGLDLIGCDLVEVSPPYDTTGNTSLLGANL 305 +DPA+APGTGTPE+GG + QA++++R G+ L+G DLVEVSPP+DT GNT+ LGA++ Sbjct: 250 FVDPAFAPGTGTPEVGGPNSFQALQVVRELAGVQLVGADLVEVSPPFDTNGNTAWLGASI 309 Query: 306 LYEMLCVLPGVVRR 319 L+EMLCV G + R Sbjct: 310 LFEMLCVSAGAISR 323 Lambda K H 0.321 0.141 0.428 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: 362 Number of extensions: 15 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: 319 Length of database: 324 Length adjustment: 28 Effective length of query: 291 Effective length of database: 296 Effective search space: 86136 Effective search space used: 86136 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 (21.8 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