Align Guanidinobutyrase; EC 3.5.3.7 (characterized)
to candidate SMc01967 SMc01967 agmatinase
Query= SwissProt::Q9I3S3 (319 letters) >FitnessBrowser__Smeli:SMc01967 Length = 352 Score = 252 bits (643), Expect = 1e-71 Identities = 134/307 (43%), Positives = 195/307 (63%), Gaps = 8/307 (2%) Query: 11 GNEMPRFGGIATMMRLPHVQSPAE---LDALDAAFVGVPLDIGTSLRSGTRFGPREIRAE 67 G + + GI T + PH+ A+ L A +GVP+D+G + R G+RFGPR +RA Sbjct: 40 GTRLAPYSGIPTFLTAPHMPVDADDPDFGNLQVAMIGVPMDLGVTNRPGSRFGPRALRAI 99 Query: 68 SVMIRPYNMATGAAPFDSLNVADIGDVAINTFNLLE-AVRIIEQEYDRILGHGILPLTLG 126 I PYN G AP L VADIGDV + LE + IE+ +I+ G+LPL++G Sbjct: 100 E-RIGPYNHVLGCAPVHDLRVADIGDVPFRSRYRLEISHEDIEKRISQIVDAGVLPLSVG 158 Query: 127 GDHTITLPILRAIKKKHGKVGLVHVDAHADVNDHMFGEKIAHGTTFRRAVEEDLLDCDRV 186 GDH+IT PIL+A+ +K VG++H+DAH D K HG FR AV + +LD RV Sbjct: 159 GDHSITHPILKAVGRKQ-PVGMIHIDAHCDTGGAFDLTKFHHGGPFRNAVLDGVLDPTRV 217 Query: 187 VQIGLRAQGYTAEDFNWSRKQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDIDG 246 +QIG+R +F++ + G V+ AEE + ++ + ++ VG GP YLSFD+D Sbjct: 218 IQIGIRGSAEYLWEFSY--ESGMTVIHAEEVTGLGIPAIIEKAKKIVGDGPTYLSFDVDS 275 Query: 247 IDPAWAPGTGTPEIGGLTTIQAMEIIRGCQGLDLIGCDLVEVSPPYDTTGNTSLLGANLL 306 +DP++APGTGTPE+GGLTT + +E+IRG +G++L+G D+VEV+P YDTT NT+ GA +L Sbjct: 276 LDPSFAPGTGTPEVGGLTTREVLELIRGLKGVNLVGGDVVEVAPQYDTTTNTAHAGAQVL 335 Query: 307 YEMLCVL 313 +E+L ++ Sbjct: 336 FEILSLM 342 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: 380 Number of extensions: 19 Number of successful extensions: 5 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: 352 Length adjustment: 28 Effective length of query: 291 Effective length of database: 324 Effective search space: 94284 Effective search space used: 94284 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: 49 (23.5 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