Align guanidinobutyrase subunit (EC 3.5.3.7) (characterized)
to candidate GFF30 PGA1_c00300 guanidinobutyrase
Query= metacyc::MONOMER-11557 (320 letters) >FitnessBrowser__Phaeo:GFF30 Length = 326 Score = 134 bits (337), Expect = 3e-36 Identities = 93/304 (30%), Positives = 152/304 (50%), Gaps = 13/304 (4%) Query: 23 GIATMLRLPHLQSAKGLDAAFIGVPLDIGT-SLRSGTRFGPRQIRAESVMIRPYNMATGA 81 GI T+ R P+L G D A +GVP G + GPR +R S + R + Sbjct: 17 GIPTLFRCPNLP-VDGQDIALVGVPHSAGNGTTERDQHLGPRALRNVSSVQRRMHSGFQL 75 Query: 82 APFDSLSVADIGDVAINTFN-LLDAVRIIEEAYDEIVEHNVIPMTLGGDHTITLPILRAL 140 P+++ + D+GDV N D ++ I Y +I + P+++GGDH+IT I++AL Sbjct: 76 DPWNAAKIVDLGDVPFPKANDNEDCIQQITNFYQQIDKAGARPVSVGGDHSITGGIVQAL 135 Query: 141 H----KKHGKIGLVHIDAHADVN---DHMFGEKIAHGTTFRRAVEEGLLDCDRVVQIGLR 193 K I +H+DAH DV DH G K + ++G +D +QIG+R Sbjct: 136 GCGAITKGEPICFLHLDAHTDVFTKVDHFLGAKKSAAHWGAYLADQGKVDPAHSMQIGIR 195 Query: 194 AQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDIDGIDPAWA 253 T D S G+ VV ++ + L ++A+V E + G PVY++FD+D +DP A Sbjct: 196 GHARTLDWLQPSYEYGYNVVTMKDYRRRGLADVVAQVTEVLAGRPVYITFDLDCLDPTIA 255 Query: 254 PGTGTPEIG--GLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGN-TSLLGANLLFEM 310 PG E G G A+ ++ G++++G D+V + P D+ T+L ++FE+ Sbjct: 256 PGVSNIEAGEKGFGIDDAVGLLHAVRGMNIVGGDVVCMMPTKDSPNQITALTAGAIMFEI 315 Query: 311 LCVL 314 + ++ Sbjct: 316 ISMI 319 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: 263 Number of extensions: 12 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: 326 Length adjustment: 28 Effective length of query: 292 Effective length of database: 298 Effective search space: 87016 Effective search space used: 87016 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